Coastal River Systems
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The Homosassa River, located in western Citrus County, is a spring-fed system within the Chassahowitzka Coastal Strip.
This area, which has elevations of 3 m or less, rapidly transitions into an extensive marsh complex which borders the
Gulf of Mexico. Development along this river is extensive with residential homes and river front businesses.
The river runs west approximately 5 km from the main spring complex to the beginning of the associated coastal marsh
complex and then another 7 km to the Gulf of Mexico. The upper portion of the Homosassa River, above the confluence with
the Halls River (which is also spring-fed; see Jones et al. 1997) is narrower, i.e. approximately 70 m in width. Below
the confluence, stream width increases to approximately 150 m or more. Above the marsh complex, mid-stream channel depth
averages 2.3 m (Frazer et al. 2001a).
The majority of stream discharge emanates from a main spring boil. Smaller spring runs in the upper river contribute
additional flow (Jones et al. 1997). Tidal cycles influence both spring discharge and flow within the river (Yobbi and
Knochenmus 1989). The average discharge between 1998 and 2000 below the main spring was reported by Frazer et al. (2001)
to be 4.6 m3 s-1. This value agrees well with the longer-term combined discharge measures reported
by Jones et al. (1997) for the main spring and all smaller springs in the upstream complex, i.e. approximately 4.9 m3
The substrate within the Homosassa River is comprised primarily of sand and mud, though small, low-relief limestone
outcrops are common and occur along the length of the river (Frazer et al. 2001a). Historically, the Homosassa River was
heavily vegetated (see Wolfe et al. 1990) and in the late 1960s was reported to be infested with Eurasion watermilfoil, Myriophyllum
spicatum (Blackburn and Weldon 1967). More recent work in this system indicates that this is no longer the case (see
Frazer et al. 2001a). In comparison to the Weeki Wachee and Chassahowitzka rivers elsewhere described, submersed aquatic
vegetation is relatively sparse. In fact, submersed aquatic vegetation was absent in 47% of locations sampled in the
Homosassa River in 2000. At those stations where submersed aquatic vegetation did occur, filamentous macroalgae (primarily
Lyngbya sp.) occurred most frequently and was the primary contributor to the overall vegetative biomass. The
non-native macrophyte, Myriophyllum spicatum, although less abundant was still the dominant macrophyte in the
The marsh complex in the lower river is extensive and water clarity is substantially reduced in this area. Salinities
are elevated in comparison to those recorded further upstream (see Yobbi and Knochenmus 1989 and Frazer et al. 2001a)
and the river takes on a more estuarine character. The reduced light environment and high salinity water are not
favorable for the growth of submersed aquatic vegetation (see Hoyer et al. 2004). Water clarity increases again with
distance seaward of the mouth. Dense patches of seagrass characterize the nearshore coastal waters (Frazer and Hale 2001,
Greenawalt et al. 2004). Unattached macroalgae can be seasonally abundant (Frazer pers. obs.). Low-relief rocky outcrops
are present, but are less abundant than in other sampling areas further south along the coast (Frazer et al. 1998).
Groundwater emanating as spring discharge is the primary water source for the Homosassa, river. Water temperatures,
as a consequence, are fairly stable in the uppermost portions of the three rivers. In fact, mean recorded water
temperatures at the upper most river transects for all rivers varied by less than 1°C across the two sampling
intervals (N=66) with a range of 23.2 to 23.9 °C. Variations in surface water temperature become more pronounced
downstream as a result of atmospheric warming or cooling, and are particularly variable in the mixing zones seaward of
the marsh complex.
The Homosassa River is sufficiently wide that terrestrial canopy coverage has little influence on incoming solar
radiation (see Frazer et al. 2001a). Within the two project periods, mean water temperatures were fairly uniform between
transects 1 and 10. Variation around the calculated mean values increased with distance downstream and was most
pronounced in the lower river, due, in large, part to tidal exchange with water from the Gulf of Mexico which exhibits
extreme seasonal variability (see Frazer et al. 1998). Overall, water temperatures were significantly lower (ANOVA, df =
19, F = 58.38, p < 0.001) between 2003 and 2005 than between 1998 and 2000.
The rate of water movement through aquatic systems can have a profound effect on their physical and biological
structure. With regard to the biological structure of rivers and streams, it is generally considered that water velocity
is the most important environmental factor affecting the abundance and distribution of plants and animals (see Allan
1995). With respect to our interest here, it should be noted that stream velocity determines not only the water
residence time, but also the substrate characteristics (see below) which are also primary determinants of the abundance
and distribution of aquatic plants and algae (Butcher 1933; Canfield and Hoyer 1988b).
The Homosassa rivers is a low gradient coastal stream with slow to moderate stream velocities (see Hoyer et al. 2004).It
is tidally influenced with flow reversals common in the lower portions, particularly in the marsh complexes. Reverse
flows were evident sometimes in the upstream areas. The directional changes in flow are important as that they can
affect increases in water residency time, particularly in the lower river and marsh transition zones, which can lead to
the accumulation of phytoplankton biomass. In addition, tidally induced flow reversals introduce relatively high
salinity water into the rivers that, in turn, can affect the species composition of plants and algae and influence their
broad patterns of abundance and distribution (Hoyer et al. 2004). In many instances, however, it is not the direction of
flow that is important, but the absolute velocity of flow. High water velocity, whether occurring as a consequence of
water moving downstream or an incoming tide, has the capacity to influence the substrate characteristics and also the
colonization capabilities of certain plants and algae. Low flow rates, coupled with increased nutrient concentrations,
may promote the accumulation of periphyton associated with submersed aquatic vegetation (including native macrophytes)
in the rivers with negative consequences. All of the scenarios above are relevant to this investigation and are
discussed in later sections of the text where appropriate.
Within the marsh transition zones of the Homosassa river, reverse flows due to incoming tides during sampling
resulted in average negative values at several transect locations on several occasions. Highest mean flows (greater than
0.3 m s-1) among the three systems were most frequently measured in the narrowest regions. Lower mean flows (<
0.10 m s-1) were generally observed in the Homosassa system. Flow rates were lower during the 1998 to 2000
project period when compared to the 2003 to 2005 project period. Flow rates were determined only at Transects 1-15; no
data were collected from open water stations seaward of the marsh complex (Sites 16-20).
Within the Homosassa River, mean flow rates at the uppermost transect, were 0.03 and 0.05 m s-1, respectively, for
the 1998-2000 and 2003-2005 project periods. There was a significant increase in average flow rates between project
periods (ANOVA, df = 19, F = 41.16, P < 0.0001). Flow rates in the marsh and estuary varied widely (less than -0.6 to
0.7 m s-1) and reflected the fact that sampling was carried out during both ebb and flood tides.
The lower flow rates during the 1998-2000 project period can be attributed to reduced rainfall in the region, lower
recharge and subsequent declines in spring discharge.
Stream discharge is of primary interest as it affects the supply, i.e. loading rates, of nutrients to the rivers and
adjacent estuarine and coastal waters. The tidal nature of the systems investigated here, however, complicates discharge
calculations, especially in the lower portions of the rivers. Thus, only those measures made at the most upstream
transects were used in subsequent calculations of nutrient loading rates.
Increased discharge rates (and also stream velocities) in 2003-2005 can likely be attributed to increased rainfall
and subsequent recharge of the aquifer system that supplies water to the springs that, in turn, serve as the origin of
stream flow. Although rainfall data were not collected directly as part of this effort, we provide, as ancillary
information, historical rainfall data obtained from the Southwest Florida Water Management District.
The rainfall data presented are for the broader Springs Coast region which includes the watersheds of the Weeki
Wachee, Chassahowitzka and Homosassa Rivers (SWFWMD unpublished data). The time period of record (1915-2005) represents
91 years. During this time interval, the annual average rainfall was 54.97 inches (std. dev. 8.54 and 95% CI of 53.19 to
56.75 inches). It is clear from these data that the three year period between 1998 and 2000 was one of low precipitation.
In fact, the rainfall amount in 2000 was the lowest on record. In contrast, the 2003-2005 time period was relatively wet.
In fact, rainfall in each of those years was greater than the long-term average of 54.97 inches per year.
The bottom sediment was dominated by sand and mud or a combination of the two substrate types as is characteristic of
low-gradient systems (Allan 1995). These substrate types are considered, in most cases, favorable for the colonization
and growth of rooted plants, and historically, the Homosassa, rivers was presumed to be dominated by native macrophyte
species such as Vallisneria americana and Sagitarria kurziana.
Qualitatively, the frequency of observed substrate types was similar during both project periods, i.e. 1998-2000 and
2003-2005. The minor differences observed among years can likely be attributed to sampling variability and appear to be
little reason for concern. With that said, however, there has been no attempt to more rigorously assess the sediments
with respect to mineral composition, organic matter content or other chemical characteristics that may affect the
ecology of these systems. In fact, increased organic matter content as a consequence of increased primary production and
subsequent decay of plant and or algal material should be a concern in any system that has been subjected to increased
With regard to the Homosassa river, slow to moderate flows coupled with the accumulation of fine grain organic
material and other organic detritus could lead to increased biological oxygen demand altering sedimentary chemical
fluxes that, in turn, mediate biological and ecological processes. For example, an enhancement of sulfate reduction
rates in vegetated sediments (Holmer and Nielsen 1997; Holmer et al. 2003) as a consequence of increased organic carbon
input (and associated increased biological oxygen demand) may induce a negative feedback on the plants themselves, as
sulfate reduction results in the release of sulfide, which can be toxic (e.g., Terrados et al. 1999). Increases in the
spatial extent or frequency of occurrence of anoxia and/or hypoxia at the sediment/water interface can also affect the
abundance and distribution of faunal organisms and may result indirectly in altered predator/prey dynamics of key
species (see, for example, Eby et al. 2005, Eggleston et al. 2005). It is worth noting that on several occasions during
our sampling effort, we observed bottom oxygen concentrations at or near 0 mg L-1 in the middle and lower
portions of the Homosassa river (Frazer et al. unpublished data). Such observations, in combination with the general
decline in vegetation in these rivers, are consistent with a eutrophication scenario and should compel water resource
managers to investigate further the sediment dynamics in these systems.
Light availability is not impacted substantially by terrestrial canopy coverage in the Homosassa river, and it is
unlikely that terrestrial canopy coverage is the primary determinant of submersed plant abundance or distribution. Other
factors, however, do have the potential to affect the light environment in these and other aquatic systems. Suspended
solids and dissolved organic material in the water, for example, are the primary factors affecting light transmittance (Kirk
1994). Suspended solids include such constituents as algal cells (Canfield and Hodgson 1983), non-volatile suspended
solids (Canfield and Bachmann 1981, Hoyer and Jones 1983) and detrital material (Buiteveld 1995). Because the Homosassa
river is primarily spring-fed, the terrestrial sediment load is minimal. Suspended organic material in the rivers is
generally comprised of algal cells (phytoplankton and/or dislodged periphyton) and/or plant/algal detritus. Dissolved
organic materials include plant and algal exudates that originate in the rivers and also humic and fulvic acids which
are derived from decaying terrestrial vegetation. These latter substances contribute color to the water and originate in
adjacent lowland forests and swamps as well as in the marsh complexes. Increased precipitation and subsequent discharge
of recently derived groundwater from the surficial aquifer and overland flow are expected to affect an increase in
colored dissolved organic material and associated color values. Similarly, increases in discharge and concomitant
increases in stream velocites might be expected to increase the occurrence of dislodged periphyton in the water. In
either case, light attenuation will be increased (less light).
In the Homosassa River, as in the Chassahowitzka River, mean light attenuation coefficients (Kd m-1;
averaged across years during each of the two project periods) were always less than 2.0 Kd m-1. The lowest
mean light attenuation coefficients (< 1.00 Kd m-1) were observed at the uppermost transect just below the
main spring complex during both project periods. Substantially greater mean values were observed in the lower river and
marsh transition zones. These values, however, were highly variable between years due, in large part, to episodic storm
events and fluctuations in rainfall. Nevertheless, light attenuation coefficients were significantly greater in 2003-2005
than they were in the initial project period (ANOVA, df = 19, F = 59.73, P < 0.0001).
Frazer et al. (2001a) reported that the euphotic depth was often shallower than the bottom depth in the lower portion
of both the Chassahowitzka and Homosassa rivers. This finding implied that the light environment was likely to limit the
downstream extent of submersed aquatic vegetation in these two systems. The increase in light attenuation coefficients
during 2003-2005, particularly in the Homosassa River, suggests that the downstream distributional range of submersed
aquatic vegetation may have been further restricted than in 1998-2000 and may explain, in part, the general reduction in
aquatic macrophytes in this system during the most recent sampling interval.
As indicated previously in this report, nitrate is a nutrient of particular concern. Jones et al. (1997) were, to our
knowledge, the first to document increasing nitrate concentrations in each of the spring systems investigated here.
These investigators suggested that further increases in nitrate concentrations were likely to occur as a consequence of
the lag-time associated with groundwater movement, and the fact that nitrate that had been supplied to the region for
many years was now entrained in the aquifer. The data reported herein indicate that this is, indeed, the case.
A 6% increase in the Homosassa River nitrate concentrations coupled with concomitant increases in flow rates and
calculated discharge has resulted in substantially greater nitrate loads. In fact, calculated nitrate loading rates in
the headwater regions of the Homosassa river has increased by 56%, since the 1998-2000 sampling period. These findings
are reason for concern, given the increased potential for eutrophication of downstream receiving waters, and warrant the
close attention of water resource managers. A closer inspection of the nitrate data collected during 1998-2000 and 2003-2005
is provided below.
The mean nitrate concentration at the uppermost sampling transect was 412 µgN L-1 during the 1998-2000
sampling period and 436 µgN L-1 during the 2003-2005 sampling period. Nitrate concentrations declined
steadily with distance downstream during both the first and second project periods, but mean values at any given
sampling transect landward of the open water sampling sites were always greater during the most recent sampling period,
i.e. 2003-2005. Overall, the increase in nitrate concentrations was highly significant between the two sampling periods
(ANOVA, df = 19, F = 91.40, P < 0.0001). Because plants and algae are conspicuously lower in the Homosassa River in
comparison with either the Chassahowitzka or Weeki Wachee rivers, it is likely that a biogeochemical process, e.g.,
denitrification, plays an important role in nitrate removal.
In comparison to nitrate, ammonium is a much less abundant chemical species in the river. Concentrations are, in fact,
typically more than an order of magnitude less than nitrate concentrations.
In the Homosassa River, mean ammonium concentrations were typically between 30 and 50 µgN L-1
regardless of location or project period. These values, although greater than those in the other two river systems
previously described, were also much more variable. Overall, there was no significant difference in ammonium
concentrations between the 1998-2000 and 2003-2005 sampling periods (ANOVA, df = 19, F = 0.20, p > 0.05).
Soluble Reactive Phosphorus
Although much attention has been paid during the last decade to the issue of increasing nitrate concentrations in
Florida's springs, it has become evident in recent years that this is not the only nutrient of concern. Phosphorus
is another. Strong empirical relationships between phosphorus and chlorophyll were established for surface waters in the
Springs Coast region in the 1990s (Frazer et al. 1998), and subsequent experimental work indicated that phosphorus,
rather than nitrogen, often limits primary production in both riverine and coastal waters (Frazer et al. 2002). In a
related effort, Notestein et al. (2003) determined that additions of phosphate resulted in greater periphyton growth in
the Chassahowitzka River than did additions of nitrate.
In comparison to nitrate, data on phosphorus concentrations in Florida's springs or spring-fed rivers are scarce.
Thus, it is has not been possible to say definitively whether or not phosphorus concentrations have increased in a like
manner. It is not unreasonable, however, to assume that they have given that fertilizers, which have been identified as
the primary source of nitrogen in groundwater (Jones et al. 1997), are also generally comprised of phosphorus. The
analysis of the data collected between 1998-2000 and 2003-2005, to our knowledge, provided the first opportunity to
assess temporal differences in phosphorus concentrations in the Weeki Wachee, Homosassa and Chassahowitzka rivers that
may be reflective of longer-term changes in this nutrient. The findings merit the close attention of water resource
Concentrations of soluble reactive phosphorus, a biologically available constituent of the total phosphorus pool,
increased significantly in all three river systems between the two project periods. In the upper regions of the Weeki
Wachee River, mean soluble reactive phosphorus concentrations increased by as much as 21% since the 1998-2000 sampling
period. Corresponding increases of 19% and 15% were documented in the upper regions of the Chassahowitzka and Homosassa
rivers, respectively. As a consequence of increased discharge, loading rates calculated at the uppermost sampling
transects in the Weeki Wachee, Chassahowitzka and Homosassa rivers increased by 33%, 44% and 46%, respectively, between
the 1998-2000 and 2003-2005 sampling periods. A closer inspection of the soluble reactive phosphorus data collected
during 1998-2000 and 2003-2005 are provided below.
In the Homosassa River, mean soluble reactive phosphorus concentrations during both project periods were highest just
below the main spring complex, and approached 19 µg P L-1. Between Transect 1 and 7, soluble reactive
phosphorus concentrations declined steadily, but remained fairly uniform in the lower freshwater portions of the river
and through the marsh transition zone, irrespective of the sampling interval. Mean values for any given sampling
transect within this broad section of the river were, with only one exception, greater in the 2003-2005 project period
than in the 1998-2000 project period. Seaward of Transect 15, soluble reactive phosphorus concentrations exhibited a
secondary decline, presumably due to the rapid assimilation of this limiting nutrient by phytoplankton in the open water
sites within the estuary (see Frazer et al. 2001a and Frazer et al. 2002). Overall, the increase in soluble reactive
phosphorus concentrations between the two project periods was highly significant (ANOVA, df = 19, F = 77.19, P <
The vast majority of the nitrogen supplied to the rivers investigated here is in the form of nitrate. Total nitrogen
concentrations increased in the Homosassa river between the 1998-2000 and 2003-2005 project periods (ANOVA, df = 19, F =
46.76, p < 0.0001 and F = 78.70, p < 0.0001, respectively). Initial declines in total nitrogen were observed in
the upper portions of the river coincident with the drawdown of nitrate. Within the Homosassa River, total nitrogen
concentrations were generally more uniform in the downstream portions of the river. It should be noted, however, that
the plant and algal biomass in this river is substantially less than either the Chassahowitzka or Weeki Wachee rivers.
Statistically significant differences in total phosphorus concentrations were observed between the two project
periods, i.e. 1998-2000 and 2003-2005. Little variation in total phosphorus concentrations was observed between years at
the uppermost sampling transects, indicating that differences were due largely to differences downstream.
The Homosassa River system exhibited an overall significant increase in total phosphorus concentrations between the
1998-2000 and 2003-2005 project periods (ANOVA, df = 19, F = 45.03, p < 0.0001). Mean total phosphorus concentrations,
although fairly uniform in the middle and lower portions of the river, were consistently higher at Transects 5 - 15
during the 2003-2005 project period than in the 1998-2000 project period.
Mean salinities over the course of this investigation were fairly uniform within each of the rivers above their
respective marsh transition zones. Mean salinities increased sharply in each of the systems as water flowed through the
marsh transition zones and into the estuary as a consequence of mixing with more saline water from the Gulf of Mexico.
Overall, salinities were significantly less in 2003-2005 than in 1998-2000 (ANOVA, p < 0.0001 for all three rivers).
This finding is consistent with the increase in rainfall and corresponding increases in flow rates and discharge that
occurred during the more recent sampling interval, i.e. 2003-2005.
Total Alkalinity and pH
The three rivers investigated here are alkaline, highly buffered systems, and are similar in this regard to many of
Florida's spring-fed systems (Beck 1965; Canfield and Hoyer 1988a). Although several statistically significant
differences in total alkalinity (mg L-1 of CaCO3) and pH were evident between the 1998-2000 and
2003-2005 project periods, we suggest that the actual magnitude of the differences were not sufficiently large to
warrant concern from either a biological or ecological perspective. Such differences are, in fact, to be expected as
dissolution of carbonate minerals in karst aquifers results in rapid and extensive interactions of surface and ground
water. The intricacies of these interactions are not fully understood, but are likely influenced by variations in
climate and the hydrologic regimes unique to each of the systems.
Low dissolved oxygen concentrations in ground water emanating as spring discharge are not uncommon (see Rosenau et al.
1977). In each of the three rivers investigated here, dissolved oxygen concentrations were always lowest at the upper
sampling transects in closest proximity to the main spring vents. Dissolved oxygen concentrations, however, increased
rapidly with distance downstream, due to atmospheric exchange and oxygen liberation by submersed aquatic vegetation (see
Frazer et al. 2001a). The daytime surface water measurements of dissolved oxygen concentration reported herein appear to
indicate that each of the three systems is well oxygenated during the day; overall mean dissolved oxygen concentrations
always exceeded 6 mg L-1. There was no significant difference in the dissolved oxygen concentration in the
Homosassa River (ANOVA, df = 19, F = 181.62, p < 0.0001).
It is important to recognize that all oxygen measures reported here were made just below the surface during daylight
hours. Thus, they are likely higher than similar measures would have been if taken just before dawn. It is also likely
that measures near the bottom sediments would have been lower, particularly in the lower portions of the rivers. In fact,
we have recently measured dissolved oxygen concentrations near 0 mg L-1 in the lower Homosassa River in areas
above the marsh transition zone (Frazer et al. unpublished data). These extremely low values may be due to an
accumulation of organic matter and respiration by the associated microbial communities. Given the concerns over nutrient
enrichment and potential eutrophication of these rivers, these ancillary observations of anoxic conditions merit further
As indicated by Frazer et al. (2001a), the physical nature of the Homosassa river is such that the phytoplankton
biomass would not be expected to accumulate in the system. Stream lengths between the main spring or complex of springs
where flow originates and the marsh complex is less than 7 km and calculated water residence times in the upper portions
of each of the rivers are the order of hours; a much greater water residencytime than would be necessary to support the
development of a substantial population of phytoplankton. With that said, however, elevated chlorophyll (a proxy measure
for phytoplankton biomass) concentrations (>10 µg L-1) have been previously documented in the lower
portions of the Homosassa river and the respective marsh transition zones, where water residency times can presumably be
increased as a consequence of tidal forces (see Frazer et al. 2001a).
Only the Homosassa River system exhibited an overall significant increase in chlorophyll concentrations between the
1998-2000 and 2003-2005 project periods (ANOVA, df = 19, F = 13.62, p < 0.01) (Figure 58). As this river has markedly
less vegetation than the other systems, it is possible that nutrients that might otherwise be assimilated by plants and
periphyton are more available to phytoplankton. It should be noted also that the lower Homosassa River and associated
marsh transition zone through which the river moves is wider than either the Weeki Wachee or Chassahowitzka rivers. Thus,
water residency times, though not quantified, are likely to be greater here than in the other two systems, thus allowing
more time for phytoplankton to grow and accumulate.