Final Report to the National Park Service in response to Project Statement BISC-N-011.000 

under NPS/FIU Cooperative Agreement No. CA5280-8-9038 

TOTAL AMMONIA CONCENTRATIONS IN SOIL, SEDIMENTS, SURFACE WATER , 

AND GROUNDWATER ALONG THE WESTERN SHORELINE OF BISCAYNE BAY WITH 

THE FOCUS ON BLACK POINT AND A REFERENCE MANGROVE SITE 

John Meeder, Ph.D. 

Joseph N. Boyer, Ph.D. 

Southeast Environmental Research Center 

Florida International University 

Miami, FL 33199 

12 February 2001 
EXECUTIVE SUMMARY 

 This study focused on ammonia as a potential stressor of marine benthic communities in 

Biscayne Bay but also included other nutrients as well. The specific tasks included in this project 

were: 1) Black Point Monitoring Program, 2) Black Point Monitoring Comparison, 3) Shoreline 

Nutrient Survey, 4) Shoreline Benthic Community Survey, and 5) Mangrove Transect 

Comparison. 

 The Black Point Monitoring Program showed that nutrient concentrations (especially 

ammonium were elevated in the canals adjacent to the landfill. The median value of unionized 

ammonia at Station 12 was 122 ppb which may be toxic to some marine fish. However, the very 

low dissolved oxygen at the same site would also preclude much marine life from thriving in 

this area. 

 The Black Point Monitoring Comparison was performed by statistical comparison of data 

from 1993 surveys with this study. No differences in water quality in the canals or nearshore 

area were found. We can clearly say that there has been no measurable improvement in water 

quality between surveys. 

 The Shoreline Nutrient Survey showed that ammonium concentrations were highest in the 

nearshore waters off Black Point, the Cutler Channel, and the Mowry Canal area. A very 

different distribution was observed for nitrate where highest concentrations were found off the 

Cutler Channel and very low levels found in the nearshore waters between Cutler Channel and 

Goulds Canal. A hot spot in total phosphorus was observed off Mangrove Key in extreme south 

Biscayne Bay. Another interesting aspect was the correspondence between sediment and water 

column nutrient levels. Levels of ammonium in the sediments are approximately an order of 

magnitude higher than the water column and generally follow each other. This was also true for 

total phosphorus although the concentrations in sediment and water were different by only a 

factor of 3. 

 Shoreline Benthic Community Survey resulted in the classification of 5 angiosperms and 22 

algal species. Among the angiosperms, Thalassia testudinum and Halodule wrightii, were the 

most common. Thalassia and Halodule did not share the same distribution or abundance 

patterns from north to south - small amounts of Halodule were found throughout the study area 

with a general increase in abundance from south to north. The inverse was true with Thalassia

abundance, which generally increased in abundance in the southerly direction. A break in 

Thalassia distribution occurred at the Goulds Canal/Black Point Area. For several km south, no 

Thalassia was reported but abundant Halodule was found in its place along with unknown green 

species, brown algae, and other noncalcareous green species. The break in Thalassia cover may 

have been partly due to salinity. Salinity during the survey increased dramatically from north to 

south, however, highest Thalassia densities occurred in the areas experiencing hypersaline 

conditions. Variability in salinity may have been important to mortality of Thalassia but salinity 

in the area between Goulds and Military Canals is not as variable as it is off the Mowry Canal. 

The only other water quality variable which may have influenced Thalassia was ammonium. 

The nearshore area between Goulds and Military Canals has the highest concentrations of 

ammonium in the water column and sediments of any site in this study. Our results indicate a 

strong correlation between elevated ammonium concentrations with 1) decreased abundance of 

Thalassia, 2) increased abundance of Halodule and fast growing algae species, and 3) the 

increase in filamentous algal cover. 
 The Mangrove Transect Comparison showed that the mangrove fringe was a source of total 

phosphorus and possibly some ammonium to the Bay, but not as much as suspected. The Bay 

itself was a source of nitrate to the mangrove fringe. 

 Understanding: 1) nutrient concentration spatial and temporal distributions, 2) the 

relationship between ammonia concentration and the level of benthic community degradation, 

and 3) the relative significance of natural nutrient addition to the system from anthropogenic or 

additional loading is paramount to establishing pollution load reduction goals. This project 

focused on the first two needs listed above to begin to establish a data base for the calculation of 

load and sources of load to Biscayne National Park. 
Acknowledgments 

 We thank all the field and laboratory technicians involved with this project especially Sean 

Gilhooly, Braxton Davis, and Amy Renshaw. We also want to thank Max Flandorfer at Biscayne 

National Park for boat time and field support. This project was possible due to funding by the 

National Park Service under NPS/FIU Cooperative Agreement No. CA5280-8-9038. Funding 

for other portions of the SERC Water Quality Monitoring Network was provided by the South 

Florida Water Management District and Everglades National Park (NPS/SERC Cooperative 

Agreement #5280-2-9017 and NPS/SFWMD Cooperative Agreement #C-7919). This is 

Technical Report #T141 of the Southeast Environmental Research Center at Florida International 

University. 
INTRODUCTION 

 Biscayne Bay is a shallow subtropical lagoonal estuary located on the southeast coast of 

Florida. The Bay is situated as a topographic basin on the surface of the Miami Limestone which 

outcrops to the west of the western shoreline forming a coastal ridge. Biscayne Bay is separated 

from the Atlantic Ocean by a series of barrier islands and limestone keys cut by shallow tidal 

passes. Biscayne Bay originated ~6,000 ybp as sea level rose during the Holocene transgression 

and has increased to a maximum depth of ~4 m during that time. The N-S orientation and 

different coastal morphology allow the Bay to be separated into three distinct regions: North, 

Central and South Bay (Card Sound). North Bay is a highly urbanized system. Channel 

dredging, the construction of Haulover Cut, and the extensive enlargement of Government Cut 

has altered circulation patterns resulting in increased salinity in this zone. 

 The western shore of Central Bay (Dinner Key to Turkey Point) was originally composed of a 

mangrove fringe and extensive freshwater marshes reaching to the foot of the coastal ridge 

several miles inland. These freshwater marshes were maintained by local rainfall and Everglades 

discharge via the transitional glades. After the turn of the century the transverse glades were 

channeled and drained directly into Biscayne Bay which resulted in saltwater encroachment. 

This was identified by the early 1940's and control structures and a coastal storm protection levee 

(L-31E) were constructed. The L-31E canal and levee system eliminated all sheet flow to 

Central and South Biscayne Bay. Canal water now enters the Bay as a point source and contains 

high levels of urban and agricultural waste creating a nutrient loading and time of delivery 

problems in the ecosystem. South Bay is relatively isolated from urban development, with the 

exception of Turkey Point Power Plant facility. Although this region has historically received 

less freshwater runoff than other areas of the Bay, it has also seen the greatest decline in 

freshwater inputs due to construction of the L-31E levee and US 1. 

 Biscayne National Park is located adjacent to large population and agricultural centers of 

Miami-Dade county. Over the past 100 years of land development, Biscayne Bay circulation 

patterns have been highly altered by management activities. Freshwater sheet flow discharge was 

replaced by channelized discharge via canals which radically changed the quantity, timing, and 

distribution of input to the Bay (Alleman et al. 1995). Because of this management activity, the 

estuarine zone of Biscayne Bay has been much reduced. 

 In conjunction with the changes in quantity, timing, and distribution of freshwater there have 

been changes in quality of the input. The water quality of both canal and groundwater inputs has 

declined as urbanization and agriculture have become more pronounced across the landscape. 

Numerous landfill and contaminated sites impact the groundwater that enters Biscayne Bay 

(Meeder et al. 1997). Nutrient loading estimates from the Mowry Canal to Biscayne Bay are very 

high compared to the typically low levels (oligotrophic conditions) found in other areas (Meeder 

et al. 1997). The addition of groundwater nutrient inputs to the model suggests that Biscayne 

Bay may be undergoing considerably more nutrient loading than previously thought (Meeder et 

al. 1997). This poses not only an environmental degradation problem but one of potential 

ammonia toxicity. As a consequence, the nearshore aquatic environment has displayed 

symptoms of decreased primary productivity and offshore migration of desirable benthic 

communities (Meeder et al. 1997). 

 This study focuses on ammonia as a potential stressor of marine benthic communities. 

Coastal mangroves are highly productive systems that are known to export ammonia because of 
microbial N2 fixation associated with aerial roots (Boto and Robertson 1990) and anaerobic 

decomposition processes (Peligri and Twilley 1999). Ammonia production in the coastal 

mangrove system is limited to a fraction of the biomass turnover on an annual basis and is 

therefore fixed within rather narrow bounds at any site (Boto and Robertson 1990; Lara and 

Dittmar 1999). In addition, most mangrove swamps along the western shore of Biscayne Bay 

grow in carbonate marl soil, about 1 m thick, which overlies the bedrock (and groundwater). 

This mud layer is relatively impermeable and separate the surficial interstitial soil and tidal water 

from the terrestrial groundwater from the watershed. This means that ammonia derived from 

inner mangrove forests is separate from anthropogenic derived ammonia in groundwater until 

they discharge into the Bay. An exception to this may be the thin fringing mangrove zone along 

the waters edge which frequently are not underlain by the marl soil horizon. This is the zone of 

highest productivity, greatest physical export of detritus, greatest belowground biomass 

production (actually accretion), and soils with the best gas exchange. 

 Groundwater nutrient levels obtained 50 m from shore along Biscayne Bay from the Dinner 

Key to Mowry Canal have total ammonia concentrations 30 or more times greater than those of 

overlying surface waters (Meeder et al. 1997). In addition, highest groundwater concentrations 

were found at Black Point and decreased by nearly half both northwards and southwards (Meeder 

et al. 1997). The location of the highest concentrations off Black Point was no surprise because 

the site is located close to the old and present Dade County landfills. 

 Only limited data on Biscayne Bay ammonia concentrations is available for inshore areas. 

The need to understand the distribution of ammonia in Biscayne National Park is necessary to 

establish pollution guidelines based upon real spatial and temporal distributions and their impacts 

to Bay ecology. A restudy of the Black Point area will aid in the determination if remedial 

environmental protection activities at the landfill have succeeded in lowering the nutrient 

concentrations delivered to the Bay. Comparisons between the Black Point area and the 

mangrove reference site should also aid the Park in determining the background levels of 

ammonia expected from coastal mangroves in contrast to ammonia levels associated with 

anthropogenic activities. 

The specific tasks included in this project were: 

 Task 1 - Black Point Monitoring Program 

Task 2 - Black Point Monitoring Comparison 

Task 3 - Shoreline Nutrient Survey 

Task 4 - Shoreline Benthic Community Survey 

Task 5 - Mangrove Transect Comparison 

 The Black Point Monitoring Program (Task 1) was designed to produce a monthly 

characterization of nutrient concentrations in the receiving waters surrounding the landfill. 

Comparisons between previous (Jones 1994) and current nutrient levels at Black Point (Task 2) 

indicated if remedial activities for the protection of the Bay from excess nutrient loading have 

been successful. 

 The purpose of the Shoreline Nutrient Survey (Task 3) was to produce a high resolution map 

of ammonia along the western BNP shoreline and to point out any hot spots within the 

mangroves, surface water, and marine sediments. This data was then combined with the ongoing 
Biscayne Bay Water Quality Monitoring Program operated by SERC and funded by SFWMD to 

produce a more generalized “snapshot” of nutrient levels in the Bay. 

 The concurrent Shoreline Benthic Community Survey (Task 4) was designed to provide a 

high resolution map of plant community structure along the west coast. Comparisons between 

benthic community characteristics and ammonia levels in water and sediments were proposed to 

develop an impact gradient curve of the relationship between ammonia levels and degree of 

community degradation. Documentation of the distribution of ammonia levels and their impacts 

on the benthos would then be used in the development of non-degradation criteria for BNP 

waters. 

 The comparison of mangroves at Black Point and the reference site (Task 5) is designed to 

determine whether there is a difference between ammonia levels found in natural and impacted 

areas. The transect data will provide a source gradient by which we can calculate the relative 

magnitude of ammonia input to the system via mangrove fringe. 
METHODS 

Task 1 - Black Point Monitoring Program

 The Black Point Monitoring Program was conducted monthly for one year at six canal 

surface water sample sites and two terrestrial sites (Fig 3). Most of these sites were the same as 

those sampled in the previous Black Point study (Jones 1994) in order to allow a direct 

comparison between data sets (Task 2). The purpose of this component is to determine the 

magnitude and extent of any ammonia source gradient from the landfill site. In addition, two soil 

sites were established along the east side of the landfills, on separate sides of the canal. 

 We decided to measure other nutrient variables along with ammonium in order to ascertain if 

the landfill had an impact on them as well. This decision was made with best science in mind. 

However, because of the increased costs, we were restricted to conducting only one shoreline 

ammonia and benthic survey instead of the proposed two. 

 Surface and bottom salinity (psu) and temperature (oC) were measured using a combination 

salinity-conductivity-temperature probe (Orion model 140). Dissolved oxygen (DO, mg l-1) was 

measured 10 cm below the surface using an oxygen electrode (Orion model 840) corrected for 

salinity and temperature. 

 Water samples were collected in sample-rinsed HDPE bottles using standard SERC 

procedures. Interstitial water of soils and sediments for the Shoreline Nutrient Survey were 

collected by vacuum lysimeter. Soil and sediment were collected by coring. Duplicate, 

unfiltered water samples were collected using 3x sample rinsed 120 ml HDPE bottles for analysis 

of total constituents. Duplicate water samples for dissolved nutrients were collected using 3x 

sample rinsed 150 ml syringes which were then filtered by hand through 25 mm glass fiber filters 

(Whatman GF/F) into 3x sample rinsed 60 ml HDPE bottles. 

 Unfiltered water samples were analyzed for total organic carbon (TOC), total nitrogen (TN), 

total phosphorus (TP), total silicate (Si(OH)4), and turbidity. TOC was measured by direct 

injection onto hot platinum catalyst in a Shimadzu TOC-5000 after first acidifying to pH<2 and 

purging with CO2-free air. TN was measured using an ANTEK 7000N Nitrogen Analyzer using 

O2 as carrier gas to promote complete recovery of the nitrogen in the water samples (Frankovich 

and Jones 1998). TP was determined using a dry ashing, acid hydrolysis technique (Solórzano 

and Sharp 1980). TS was measured using the molybdosilicate method (Strickland and Parsons 

1972). Turbidity was measured using an HF Scientific model DRT-15C turbidimeter and 

reported in NTU. 

 Filtrates were analyzed for soluble reactive phosphorus (SRP), nitrate+nitrite (NOx), nitrite 

(NO2

-

), and total ammonia (NH4

+

) on a four channel autoanalyzer (Alpkem model RFA 300). 

All analyses were completed within 28 days after collection (except for NH4

+

, which was run the 

following day) in accordance to standard SERC laboratory quality control guidelines. 

 Some parameters were not measured directly, but were calculated by difference. Nitrate 

(NO3

-2) was calculated as NOX-

 - NO2

-

, dissolved inorganic nitrogen (DIN) as NOX + NH4

+

, and 

total organic nitrogen (TON) defined as TN - DIN. All concentrations are reported as ppm-N or 

P unless noted. All elemental ratios discussed were calculated on a molar basis. 
Task 2 - Black Point Monitoring Comparison

 Data from Jones (1994) and current programs were compiled and analyzed by station using 

the Mann-Whitney U test; the nonparametric version of the two group unpaired t-test. 

Significance was set at P<0.05. 

Task 3 - Shoreline Nutrient Survey

 During the 1998 dry season, nutrient concentrations in nearshore surface water (~50 m 

offshore), marine sediment pore water (~50 m offshore), mangrove soils (~25 m onshore), and 

mangrove surface waters (~25 m onshore) were sampled approximately every 1 km along the 

west shoreline for a total of 22 (Fig 2). We also sampled near canal mouths and at significant 

features. Data from the Shoreline Nutrient Survey were combined with data from the FIU water 

quality monitoring program for Biscayne Bay. All data was collected in the same month and 

presented as kriged contour plots (Surfer, Golden Software). 

Task 4 - Shoreline Benthic Community Survey

 The Shoreline Benthic Community Survey was conducted in conjunction with the Shoreline 

Nutrient Survey. Benthic plant community structure was characterized in three plots (0.25 m2

) 

within one meter of each Shoreline Ammonia Survey sampling site. The number of shoots of 

marine plants was counted, measured, and weighed in subplots within each of the three plots. 

Plant taxa and their abundance were recorded using the Braun-Blanquet survey method 

(Fourqurean et al. 2000). Species presence, percent cover, and community structure along with 

distance from shore, water depth, soil depth and type, salinity, and other parameters was also 

recorded. Epiphyte percent cover was recorded on the larger plant leaves and bay bottom at each 

plot. Data were analyzed by standard methods employed in earlier studies (Meeder et al. 1997). 

Task 5 - Mangrove Transect Comparison

 The Mangrove Transect Comparison was structured so as to provide information concerning 

nutrient inputs from mangrove forests in Biscayne Bay. The sampling area was selected based 

upon several criteria: 1) low range of ammonia concentration, 2) lack of known anthropogenic 

source of ammonia, and 3) similar type mangrove system as found at Black Point (narrow fringe 

with wide basin). Five sites were sampled: a upstream mostly freshwater distribution canal (DC) 

which was 640 m west of the coast and 300 m north of the Mowry Canal; a site east of DC in the 

mangrove fringe (TF); a site just offshore TF (TBB); a mangrove fringe site 500 m south of the 

Military Canal (CF); and a corresponding offshore site (CBB). At each site, surface water and 

soil or sediment were sampled and analyzed for nutrients as above on a monthly basis for one 

year. 
RESULTS 

Task 1 - Black Point Monitoring Program

 Summary of results from the monthly Black Point Monitoring Program are shown in Table 1. 

For the period of record, salinity ranged from 0.02 – 39.7 psu; temperature from 20.9 – 31.6 oC, 

DO from 0.2 – 11.4 mg l-1, pH from 6.90 – 8.78, NH4

+

 from 0.004 – 26.97 ppm, and NH3 from 

0.0 – 654 ppb. Additional nutrient values also showed large ranges: NO3

-2 from 0.002 – 0.415 

ppm and TP from 0.002 – 0.94 ppm. These large ranges are indicative of terrestrial/groundwater 

nutrient loading to the canals and inshore areas of Biscayne Bay. 

 Monthly maps of NH4

+

 concentration plotted by station are presented in Figs. 3-14. 

Concentrations are on log scale because the range in data was so large. Highest NH4

+

concentrations routinely occurred at Sta #12 which is directly downstream of the landfill. Sta. 

#12 also had highest DOC, NO2

-

, NH3, SRP, and lowest DO levels. The median value of NH3 at 

#12 was 122 ppb which may be toxic to some marine fish. However, the very low DO at the 

same site would also preclude much marine life from thriving in this area. 

 Differences among stations were shown as box-and-whisker plots (Fig. 15 & 16). The boxand-whisker plot is a powerful statistic which displays the median, range, and the shape of the 

data distribution. Water quality variable distributions are usually skewed to the right (nonnormal) so it is more appropriate to use the median as the measure of central tendency. The 

central, horizontal line of the box is the median of the data, the top and bottom of the box are the 

25th and 75th percentiles (quartiles), the ends of the whiskers are the 10th and 90th percentiles, 

and any points outside (<10th and >90th percentiles) may be considered outliers (suppressed in 

the graphs). The box-and-whisker plot also serves as a graphical, nonparametric ANOVA. The 

notch in the box is the 95% confidence interval of the median. When notches among boxes do 

not overlap, the medians may be considered significantly different. 

 Comparing the canal sites (#10, 11, 12, & 13) to the nearshore sites (#14 & 15) it becomes 

clear that the nearshore sites have higher salinity, pH, and a narrower range in nutrients. We 

should point out that station #14 was located in the water column above two groundwater wells 

in ~1 m of water. Water quality at this site may have been influenced by seepage from these 

wells as they had positive hydraulic pressure at all times of sampling. The shallow well had 

significantly higher NO3

-2 and lower salinity than the deep well (data not shown). From this we 

may imply that groundwater in the shallow well was derived more from surface water than the 

deep well, which has been previously confirmed by Meeder et al. (1997). Both wells had 

significant amounts of NH4

+

 present; generally an order of magnitude greater than un-impacted 

surface waters. 

Task 2 - Black Point Monitoring Comparison

 Statistical comparison of data from 1993 surveys with this study resulted in no significant 

difference (P>0.05) in water quality variables in the canals or nearshore (Fig. 17-20). Each 

station was treated separately using a Mann-Whitney U test; the nonparametric version of the two 

group unpaired t-test. What was noticeable was that the ranges in the data of the current study 

were larger than found in the previous study. This was probably the result of climactic influence 

such as higher rainfall in 1998-99. We can clearly say that there has been no measurable 

improvement in water quality between surveys. 
Task 3 - Shoreline Nutrient Survey 

 This survey was conducted in April 1998 which happened to occur at the end of a very dry 

season. Salinity in southern Biscayne Bay was elevated in both nearshore and offshore areas 

(Fig. 21) as a result of this. Ammonium concentrations (Fig. 22) during this period were highest 

in the nearshore waters off Black Point (0.035 ppm), the Cutler Channel (0.148 ppm), and the 

Mowry Canal area (0.013 ppm). NH3 was also elevated in these areas (Fig. 23) being 3.6, 2.4, 

3.1 ppb, respectively. A very different distribution was observed for NO3

-2 (Fig. 24) with highest 

concentrations being found off the Cutler Channel (0.148 ppm) and very low levels found in the 

nearshore waters between Cutler Channel and Goulds Canal. A hot spot in TP (0.0519 ppm) was 

observed off Mangrove Key in extreme south Biscayne Bay (Fig 25). Otherwise, TP 

concentrations were very low (<0.015 ppm) throughout the Bay. TOC (Fig. 26) and TON (Fig. 

27) showed similar high nearshore – low offshore gradients. Highest TOC (12.2 ppm) and TON 

(1.6 ppm) concentrations occurred off the mangroves between Cutler Channel and Goulds Canal. 

There was also a local increase in TON between Goulds and Military Canals. 

 Another interesting aspect of the Shoreline Nutrient Survey was the correspondence between 

sediment and water column nutrient levels. Figure 28 shows the NH4

+

 concentration in water 

and sediment along the coast from north to south. Levels of NH4

+

 in the sediments are 

approximately an order of magnitude higher than the water column and generally follow each 

other. This was also true for TP (Fig. 29) although the concentrations in sediment and water 

were different by only a factor of 3. 

 Interestingly, the area around Black Point which showed high NH4

+

 from the landfill had a 

corresponding depression in TP. This may be because of increased biological demand for P from 

the external supplement of N. 

Task 4 - Shoreline Benthic Community Survey

 Table 2 is a list of marine plant taxa reported in this study. Taxa were included only when 

found in more than three separate plots or if they occupied more than 2% of the area in a single 

plot. This criteria excluded numerous uncommon species that carry little ecological information 

at the community level supported by literature. Five angiosperms and 22 algal species were 

recorded. Filamentous algae were not further classified. Among the angiosperms, Thalassia 

testudinum and Halodule wrightii, were the most common, the others being found only at a few 

stations. Thalassia and Halodule, although abundant at most sites, did not share the same 

distribution or abundance patterns from north to south (Fig. 30). Minor amounts of Halodule

were found throughout the study area with a general increase in abundance from south to north. 

The inverse was true with Thalassia abundance, which generally increased in abundance in the 

southerly direction. The red algae group was also more abundant in the south. Penicillus and 

most other calcareous green species displayed the same distributional pattern as Thalassia. Some 

fast growing green algae species (Acetabularia) did not exhibit obvious trends in distribution or 

abundance. Filamentous algae was not taxonomically subdivided further but was reported as 

percent cover as an epiphyte. Generally, either filamentous algae cover was low (less than 20% 

of available substrate) or significant (over 80% of available cover). Filamentous algae cover was 

highest in the area between Black Point and the Mowry Canal with minor hot spots located near 

other canal mouths. 

 A break in Thalassia distribution occurred at the Goulds Canal/Black Point Area. For several 

km south, no Thalassia was reported but abundant Halodule was found in its place (Fig. 29). 
The break in Thalassia was also associated with changes in distribution of other marine plants. 

An unknown green species, brown algae, and other noncalcareous green species increased in 

abundance where Thalassia was not present. 

 The break in Thalassia cover may have been partly due to salinity. Salinity during the survey 

increased dramatically from north to south (Fig. 31), however, highest Thalassia densities 

occurred in the areas experiencing hypersaline conditions. Variability in salinity may have been 

important to mortality of Thalassia but salinity in the area between Goulds and Military Canals is 

not as variable as it is off the Mowry Canal (Boyer, unpublished data). The only other water 

quality variable which may have influenced Thalassia was NH4

+

 (Fig. 32). The nearshore area 

between Goulds and Military Canals has the highest concentrations of NH4

+

 in the water column 

and sediments of any site in this study. It was more likely that chronic inputs of NH4

+

 were 

responsible for Thalassia loss. 

Task 5 - Mangrove Transect Comparison

 Data were analyzed using the nonparametric Mann-Whitney U Test which is comparable to 

an unpaired t Test. Some general trends were observed which are best visualized in Fig. 33. The 

distribution channel (DC) was not a source of NO3

-2, NH4+

, TP, or SRP to the mangroves. 

However, DC was a significant source of Chl a and TOC to the mangrove fringe. The mangrove 

fringe itself was a source of TP, SRP, and possibly NH4

+

 to the Bay. The Bay itself was a source 

of NO3

-2 to the mangrove fringe. 

 Nutrient concentrations in the mangrove fringe sites (TF and CF) were not significantly 

different from each other (P>0.10) so they could be pooled and treated as being representative of 

the mangrove fringe in Biscayne Bay. However, we did not do this as the Bay sites had some 

significant differences – NH4

+

 and TOC were slightly higher at CBB and NO3

-2 was lower. Most 

important was the finding that although NH4

+

 concentrations are high in mangroves, a significant 

portion of that may be derived from upland drainage. 
DISCUSSION 

 The Black Point Monitoring Program showed that nutrient concentrations (especially 

ammonium were elevated in the canals adjacent to the landfill. The median value of unionized 

ammonia at Station 12 was 122 ppb which may be toxic to some marine fish. However, the very 

low dissolved oxygen at the same site would also preclude much marine life from thriving in 

this area. 

 The Black Point Monitoring Comparison was performed by statistical comparison of data 

from 1993 surveys with this study. We found no difference in water quality in the canals or 

nearshore area between the two studies. From this we can clearly state that there has been no 

measurable, beneficial effect of remediation activities on the water quality of the Black Point 

area. 

 The Shoreline Nutrient Survey showed that ammonium concentrations were highest in the 

nearshore waters off Black Point, the Cutler Channel, and the Mowry Canal area. A very 

different distribution was observed for nitrate where highest concentrations were found off the 

Cutler Channel and very low levels found in the nearshore waters between Cutler Channel and 

Goulds Canal. A hot spot in total phosphorus was observed off Mangrove Key in extreme south 

Biscayne Bay. Another interesting aspect was the correspondence between sediment and water 

column nutrient levels. Levels of ammonium in the sediments are approximately an order of 

magnitude higher than the water column and generally follow each other. This was also true for 

total phosphorus although the concentrations in sediment and water were different by only a 

factor of 3. 

 Submerged aquatic plant communities respond to nutrient loading by the replacement of slow 

growing with faster growing species and finally by phytoplankton (Duarte 1995). In many South 

Florida water bodies heavy epiphytic algae growth replaces phytoplankton, with the same end 

result. In many cases, the indirect effect of faster growing species dominance is additional stress 

on the slower growing species by shading or light exclusion (Orth and Moore 1983). Thalassia

is replaced by Halodule in seagrass areas with increases nutrient loading (Powell et al 1991; 

Fourquerean et al 1995). In other studies Zostera marina and Ruppia were replaced by faster 

growing green algae species 

 The distribution of Thalassia and other aquatic vegetation have been linked to groundwater 

discharge in Biscayne Bay (Kohout and Kolipinski 1967; Meeder et al 1996) and other regions 

such as Yucatan, Mexico (Herrera-Silveira 1994) and Australia (Johannes 1980). Meeder et al 

(1997) found that Thalassia was not abundant in areas receiving groundwater discharge. This 

area was from the shoreline to 400 m offshore in the area between the Military and Mowry 

Canals. Benthic community distribution influenced by groundwater discharge usually form 

bands parallel to the shoreline and the effects of groundwater discharge usually decrease 

exponentially with distance offshore. However, the major source of western Biscayne Bay 

nutrient loading is canal discharge. 

 Canal discharge varies more in both nutrient concentration levels and discharge volumes 

seasonally than does groundwater. Because most canal discharge occurs during the rainy season 

with prevailing southerly or southeasterly winds canal waters most frequently pile up along the 

western shore of Biscayne Bay. Therefore low salinity, nutrient rich canal water is held along the 

shoreline. The effects of this pattern of freshwater canal discharge is hard to separate from the 

groundwater discharge pattern in terms of nearshore benthic community structure and 
productivity (Meeder et al 1997). The nutrient loading of both canal and ground water is 

significant. 

 Although ammonia toxicity or increased nutrient concentration may be responsible for the 

lack of Thalassia and slower growing algae species in the vicinity of Black Point our data does 

not unequivocally support this relationship. Our data does support a more than causal 

relationship between high NH4

+

 concentration with the lack of Thalassia, however, the nutrient 

levels may be a surrogate of other causes. For example, both high NH4

+

 and nutrient 

concentrations are related to freshwater delivery to the bay via canal and groundwater, which 

may carry other agents acting alone or synergistically with NH4

+

 and nutrients to cause toxic or 

unfavorable conditions for Thalassia and other slow growing plants. In addition, salinity 

characteristics may also play a role in Thalassia competition. 

Thalassia responds best to normal marine salinities. Salinities too high or too low or a 

rapidly changing salinity regime produce stress to Thalassia that frequently favors other species. 

Historically the northern portion of Biscayne Bay was much more estuarine in nature but has 

maintained near marine salinities since the opening of Haulover Cut and dredging of Miami 

River-Government Cut Channels which permit rapid freshwater discharge mixing and export. 

Northern Biscayne Bay also has more frequent high turbidity periods which affects light 

availability, especially in deeper portions of the Bay (Harlem 1979). The southern part of the 

Bay is less well flushed, perhaps, but has much less freshwater discharge. This is especially true 

south of North Canal. In this region salinities are always near marine conditions and can become 

slightly hypersaline during extended dry periods such as during our April sampling period. 

Normally Thalassia abundance increases from north-to-south because of more continuous near 

marine salinity and low turbidity levels in Southern Biscayne Bay. This trend is apparent when 

plotting salinity vs Thalassia abundance (Fig. 30). The break in the trend is obviously not soley 

the result of salinity. 

 The major purpose of the funding for this project was to determine if NH4

+

 levels were 

elevated enough in the waters and soils of nearshore Biscayne Bay to produce toxic affects on 

Thalassia. Previously the relationship between Thalassia distribution and salinity and nutrient 

concentrations were discussed with the conclusion that the competitive advantage of fast growing 

species over slow growing species and the resulting light competition can adequately explain the 

lack of Thalassia along the North-to-south study gradient. However, a close examination of the 

relationship between NH4

+

 concentration and Thalassia abundance indicates that in areas of 

NH4

+

 concentrations greater than 0.015 ppm excludes Thalassia. However, in these areas other 

nutrients except TP are also quite elevated and therefore NH4

+

 alone cannot be.implicated. 

 The Mangrove Transect Comparison showed that the mangrove fringe was a source of total 

phosphorus and possibly some ammonium to the Bay, but not as much as suspected. The Bay 

itself was a source of nitrate to the mangrove fringe. NH4

+

 levels in nearshore Biscayne Bay and 

in the coastal mangrove soils are often quiet high for normal surface waters but probably do not 

in themselves produce toxicity. One reason for the high concentrations may be groundwater 

inputs. Anaerobic groundwater contains high levels of NH4

+

 especially the shallow groundwater 

around the Black Point landfill. High discharge rates of 1-3 l hr-1

 m

-2 (Meeder et al. 1997) may 

supply a significant and unrecognized N load to the Bay. 
CONCLUSIONS 

 Freshwaters reaching nearshore Biscayne Bay contains numerous nutrients, metals, 

hydrocarbons, pesticides, and herbicides from anthropogenic sources. We have quantified 

nutrients with particular attention to NH4

+

. Our results indicate a strong correlation between 

elevated ammonium concentrations with 1) decreased abundance of Thalassia, 2) increased 

abundance of Halodule and fast growing algae species, and 3) the increase in filamentous algal 

cover. 

 The high salinities encountered during this study are associated with a very dry winter. 

Therefore, the effects of canal inputs on ambient nutrient concentrations are minimal during this 

period. The elevated nutrient levels observed should be considered a chronic condition. 

Conclusions can not be made that ammonia toxicity is solely responsible for the loss of Thalassia

and other slower growing algae. 
REFERENCES 

Alleman, R. W., et al. 1995. Biscayne Bay surface water improvement and management. 

Technical supporting document. South Florida Water Management District. 

Boto, K. G., and Robertson, A. I., 1990. The relationship between nitrogen fixation and tidal 

exports of nitrogen in a tropical mangrove system. Estuar., Coast. Shelf Sci. 31: 531-540. 

Duarte, C. M., 1995. Submerged Aquatic Vegetation in Relation to Different Nutrient Regimes: 

Ophelia 41: 87-112. 

Fourqurean, J. W.; Durako, M. J.; Zieman, J. C., 1999. Seagrass monitoring in the Florida Keys 

National Marine Sanctuary, Annual Report, FY 1999: FKNMS. 

Fourqurean, J. W.; Powell, G. V. N.; Kenworthy, W. J.; Zieman, J. C., 1995. The effects of 

long-term manipulation of nutrient supply on competition between the seagrasses Thalassia

testudinum and Halodule wrightii in Florida Bay: Oikos 72: 349-358. 

Frankovich, T. A., and Jones, R. D., 1998. A rapid, precise, and sensitive method for the 

determination of total nitrogen in natural waters. Marine Chemistry 60: 227-234. 

Harlem 1979. Aerial photographic interpretation of the historical changes in northern Biscayne 

Bay, Florida; 1952-1976. University of Miami, Coral Gables, FL. 

Harlin, M. M., Thorne-Miller, B., 1981. Nutrient enrichment of seagrass beds in a Rhode Island 

coastal lagoon: Marine Biology 65: 221-229. 

Herrera-Silveira, J. A., 1994. Nutrients from underground water discharges in a coastal lagoon 

(Celestun, Yucatan, Mexico): Verh. Internat. Verein. Limnol. 25: 1398-1401. 

Johannes, R. E., 1989. The ecological significance of the submarine discharge of groundwater: 

Marine Ecology Progress Series 3: 365-373. 

Jones, R. D., 1994. Biscayne Bay Ammonium Monitoring. Final Report to Biscayne National 

Park under NPS/SERP Cooperative Agreement CA-5280-8-8007. 

Kohout, F. A., and Kolpinski, M. C., 1967. Biological zonation related to groundwater discharge 

along the shore of Biscayne Bay, Miami, Florida: , Estuaries: Ecologies and Populations, 18, pp. 

488-499. 

Lara, R. J., and Dittmar, T., 1999. Nutrient dynamics in a mangrove creek (North Brazil) during 

the dry season. Mangroves and Salt Marshes 3: 185-195. 

Littler, D. S.; Littler, M. M.; Bucher, K. E.; and Norris, J. N., 1989. Marine Plants of the 

Caribbean: Smithsonian Inst. Press, Wash. D. C., 263p. 
Meeder, J. F.; Alvord, J.; Byrns, M.; Ross, M. S.; Renshaw, A., 1997. Distribution of benthic 

nearshore communities and their relationship to groundwater nutrient loading: Final Report to 

Biscayne National Park, SERP, FIU, 41p. plus figures. 

Orth, R. J., and Moore, K. A., 1983. Chesapeake Bay: An unprecedented decline in submerged 

aquatic vegetation. Science 222: 51-53. 

Peligri, S. P., and Twilley, R. R., 1999. Heterotrophic nitrogen fixation (acetylene reduction) 

during leaf litter decomposition of two mangrove species in South Florida, USA. Marine 

Biology 131: 53-61. 

Powell, G. V. N., Fourqurean, J. W., Kenworthy, W. J., Zieman, J. C., 1991. Bird colonies cause 

seagrass enrichment in a subtropical estuary: Observational and experimental evidence: 

Estuarine, Coastal and Shelf Science 32: 567-579. 

Solorzano, L., and Sharp, J. H., 1980. Determination of total dissolved phosphorus and 

particulate phosphorus in natural waters. Limnology and Oceanography 25: 754-758. 

Strickland, J. D. H., and Parsons, T. R., 1972. A practical handbook of seawater analysis. 

Bulletin of the Fisheries Research Board of Canada 167: 107-112. 

Taylor, W. R., 1972. Marine Algae of the Eastern Tropical and Subtropical Coasts of the 

Americas: Univ. Mich. Press, Ann Arbor, 870p. 

Thorhaug, A., 1976. The vascular plants of Biscayne Bay: in Biscayne Bay: Past/ Present/ Future; 

Univ. Miami Sea Grant Spec. Rpt. No. 5, pp. 95-102. 

Woelkerling, W. J., 1976. South Florida Benthic Marine Algae: Sedimenta V, Comp. Sed. Lab, 

Univ. Miami, 148p. 
Table 1. Water quality variable statistics. 

VARIABLE STA MEDIAN MIN. MAX. n 

Surface 10 0.20 0.02 1.00 12 

Salinity 11 12.00 2.20 27.10 12 

(psu) 12 11.91 1.40 29.10 12 

 13 7.80 0.20 26.10 12 

 14 22.40 5.30 37.50 8 

 15 26.45 19.20 39.70 12 

 16 5.00 0.70 23.40 3 

 17 3.30 3.30 3.30 1 

Bottom 10 

Salinity 11 20.10 12.40 37.20 11 

(psu) 12 16.40 4.00 33.70 10 

 13 19.90 4.80 36.70 12 

 14 23.60 11.80 38.00 7 

 15 26.75 19.30 39.70 12 

 16 

 17 

Surface 10 25.95 23.30 29.60 12 

Temperature 11 25.90 21.40 30.40 12 

(

o

C) 12 24.80 23.40 31.60 11 

 13 25.95 21.90 30.40 12 

 14 25.45 21.40 30.70 8 

 15 25.35 20.90 31.50 12 

 16 22.05 22.00 22.10 2 

 17 21.80 21.70 21.90 2 

Bottom 10 

Temperature 11 24.10 20.90 29.80 10 

(

o

C) 12 25.05 22.90 28.50 10 

 13 25.25 23.30 31.20 12 

 14 23.80 21.40 30.70 7 

 15 25.35 21.00 31.50 12 

 16 

 17 

Surface 10 5.70 1.10 8.10 12 

Dissolved 11 4.75 1.10 6.80 12 

Oxygen 12 3.80 0.40 5.90 11 

(mg l-1) 13 4.95 1.00 7.30 12 

 14 5.30 2.70 11.20 8 

 15 6.90 3.80 8.10 12 

 16 3.50 1.90 5.10 2 

 17 3.35 2.30 4.40 2 

 

 
VARIABLE STA MEDIAN MIN. MAX. n 

Bottom 10 

Dissolved 11 5.00 2.10 8.70 10 

Oxygen 12 2.50 0.20 6.60 10 

(mg l-1) 13 4.55 1.20 6.80 12 

 14 5.70 2.70 11.40 7 

 15 7.15 4.80 11.20 12 

 16 

 17 

pH 10 7.815 7.397 8.229 11 

 11 7.860 7.109 8.370 11 

 12 7.800 6.900 8.590 11 

 13 7.870 7.100 8.350 11 

 14 8.120 7.300 8.463 7 

 15 8.370 6.971 8.780 9 

 16 7.985 7.500 8.303 4 

 17 8.074 7.854 8.500 4 

Total 10 4.040 3.141 13.250 12 

Organic 11 6.137 3.717 17.010 12 

Carbon 12 8.663 4.797 26.358 12 

(ppm) 13 6.540 3.813 9.611 12 

 14 6.512 4.974 10.102 9 

 15 4.990 3.626 7.947 11 

 16 11.471 5.274 16.337 4 

 17 18.503 6.899 27.450 3 

NO2

-

 10 0.0070 0.0010 0.0290 12 

(ppm) 11 0.0100 0.0020 0.0300 12 

 12 0.0280 0.0080 0.1030 12 

 13 0.0110 0.0020 0.0320 12 

 14 0.0040 0.0020 0.0280 9 

 15 0.0100 0.0010 0.0510 12 

 16 0.0050 0.0030 0.0350 4 

 17 0.0060 0.0040 0.0180 3 

NO3

-2 10 0.2020 0.0190 0.4120 12 

(ppm) 11 0.1090 0.0090 0.4150 12 

 12 0.1230 0.0040 0.3870 12 

 13 0.1290 0.0140 0.3690 12 

 14 0.0950 0.0020 0.1950 9 

 15 0.0620 0.0000 0.3380 12 

 16 0.0410 0.0340 0.0820 4 

 17 0.0300 0.0020 0.0310 3 

 

 
VARIABLE STA MEDIAN MIN. MAX. n 

NH4

+

 10 0.0550 0.0170 0.3530 12 

(ppm) 11 0.2190 0.0970 0.6720 12 

 12 3.2650 0.2220 26.9730 12 

 13 0.1760 0.1030 0.7520 12 

 14 0.2110 0.0110 0.5150 9 

 15 0.0420 0.0040 0.1350 12 

 16 0.1130 0.0790 0.4810 4 

 17 0.0470 0.0370 0.0480 3 

NH3 10 0.00 0.00 0.02 12 

(ppb) 11 0.01 0.00 0.04 12 

 12 0.11 0.00 0.65 12 

 13 0.01 0.00 0.04 12 

 14 0.01 0.00 0.03 9 

 15 0.00 0.00 0.01 12 

 16 0.00 0.00 0.04 4 

 17 0.00 0.00 0.00 2 

Soluble 10 0.0040 0.0010 0.3060 12 

Reactive 11 0.0030 0.0000 0.0280 12 

Phosphorus 12 0.0040 0.0010 0.1120 12 

(ppm) 13 0.0030 0.0000 0.0190 12 

 14 0.0030 0.0000 0.0340 9 

 15 0.0020 0.0000 0.1370 12 

 16 0.0020 0.0002 0.0620 4 

 17 0.0030 0.0004 0.0060 3 

Total 10 0.0110 0.0040 0.3230 11 

Phosphorus 11 0.0100 0.0030 0.0420 11 

(ppm) 12 0.0110 0.0020 0.0300 11 

 13 0.0080 0.0020 0.0150 10 

 14 0.0080 0.0040 0.0200 8 

 15 0.0050 0.0020 0.0170 11 

 16 0.0240 0.0060 0.9400 4 

 17 0.0120 0.0060 0.0140 3 

Total 10 0.2970 0.2060 0.7020 12 

Organic 11 0.3910 0.0860 0.6080 12 

Nitrogen 12 0.0370 0.0240 0.8570 12 

(ppm) 13 0.3180 0.1420 0.5890 12 

 14 0.3560 0.1320 1.2040 9 

 15 0.3270 0.1790 0.5370 12 

 16 0.5660 0.2790 1.4580 4 

 17 0.8470 0.3310 1.9860 3 

 

 
VARIABLE STA MEDIAN MIN. MAX. n 

Si(OH)4 10 1.1840 1.1840 1.1840 2 

(ppm) 11 0.6540 0.6540 0.6540 2 

 12 0.3370 0.3370 0.3370 2 

 13 0.7390 0.7390 0.7390 2 

 14 

 15 0.0780 0.0780 0.0780 2 

 16 

 17 
Table 2. List of benthic plant taxa. 

BENTHIC PLANT 

SPECIES 

ANGIOSPERMS 

Halodule wrightii 

Halophila engelmannii 

Ruppia maritma 

Syringodium filiforme 

Thalassia testudinum 

CHLOROPHYTA 

Acetabularia crenulata 

Anadyomene stellata 

Avrainvillea nigricans 

Batophora oerstedia 

Caulerpa mexicana 

Caulerpa racemosa 

Caulerpa vertcillata 

Halimeda incrassata 

Halimeda opuntia 

Halimeda simulans 

Penicillus capitatus 

Rhipocephalus phoenix 

Udotea flabellum 

Ulva lactuca 

PHAEOPHYTA 

Dictyota cf crenulata 

Rosenvingea sanctae-crusis 

Sargassum filipendula 

RHODOPHYTA 

Acanthophora specifera 

Chondria littoralis 

Hypnea cornuta 

Hypoglossum involvens 

Laurencia intricata 
Figure 1. Map of Black Point Monitoring Program sampling sites in relation to FIU Biscayne Bay 

water quality monitoring program (+) and South Florida ecosystem. 

-80.5 -80.4 -80.3 -80.2 -80.1 25.2

25.3

25.4

25.5

25.6

25.7

25.8

25.9

26.0

-82.0 -81.5 -81.0 -80.5 -80.0

25.0

25.5

26.0

26.5

27.0

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29 2 5 .5 2

25.53

25.54

25.55

South Dade Sewage

Treatment Facility

Control Gate

1 0

11

12

13

14

15

1617

Black Point

Goulds Canal
Figure 2. Locations of Shoreline Ammonia Survey sites in relation to FIU Biscayne Bay water 

quality monitoring program and major canals. 

-80.40 -80.35 -80.30 -80.25 -80.20 -80.15 25.35

25.40

25.45

25.50

25.55

25.60

25.65

25.70

25.75

Goulds Canal

Mowry Canal

Military Canal

Cutler Channel
Figure 3. Map of NH4

+

 concentrations at landfill sites in Oct. 1998. 

Figure 4. Map of NH4

+

 concentrations at landfill sites in Nov. 1998. 

Figure 5. Map of NH4

+

 concentrations at landfill sites in Dec. 1998. 

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

14

South Dade Sewage 15

Treatment Facility

Control Gate

Oct. 1998

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

South Dade Sewage 15

Treatment Facility

Control Gate

Nov. 1998

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

South Dade Sewage 15

Treatment Facility

Control Gate

Dec. 1998

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00
Figure 6. Map of NH4

+

 concentrations at landfill sites in Jan. 1999. 

Figure 7. Map of NH4

+

 concentrations at landfill sites in Mar. 1999. 

Figure 8. Map of NH4

+

 concentrations at landfill sites in Apr. 1999. 

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

14

South Dade Sewage 15

Treatment Facility

Control Gate

Jan. 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

14

15

1617

South Dade Sewage

Treatment Facility

Control Gate

Mar. 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

13

14

South Dade Sewage 15

Treatment Facility

Control Gate

Apr. 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00
Figure 9. Map of NH4

+

 concentrations at landfill sites in May 1999. 

Figure 10. Map of NH4

+

 concentrations at landfill sites in Jun. 1999. 

Figure 11. Map of NH4

+

 concentrations at landfill sites in Aug. 1999. 

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

14

South Dade Sewage 15

Treatment Facility

Control Gate

Jun. 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

14

15

1617

South Dade Sewage

Treatment Facility

Control Gate

May 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

14

South Dade Sewage 15

Treatment Facility

Control Gate

Aug. 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00
Figure 12. Map of NH4

+

 concentrations at landfill sites in Sep. 1999. 

Figure 13. Map of NH4

+

 concentrations at landfill sites in Oct. 1999. 

Figure 14. Map of NH4

+

 concentrations at landfill sites in Dec. 1999. 

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

14

15

16

South Dade Sewage

Treatment Facility

Control Gate

Sep. 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

14

15

1617

South Dade Sewage

Treatment Facility

Control Gate

Oct. 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00

-80.35 -80.34 -80.33 -80.32 -80.31 -80.30 -80.29

25.52

25.53

25.54

25.55

10

11

12

13

South Dade Sewage 15

Treatment Facility

Control Gate

Dec. 1999

NH4 (ppm)

 0.00 to 0.01

 0.01 to 0.10

 0.10 to 1.00

 1.00 to 10.00
Figure 15. Box-and-whisker plots of water quality variables by station in the landfill canals. 

0

5

10

15

20

25

30

35

40

psu

10 11 12 13 14 15

0

5

10

15

20

25

30

35

40

psu

10 11 12 13 14 15

21

22

23

24

25

26

27

28

29

30

31

oC

10 11 12 13 14 15 21

22

23

24

25

26

27

28

29

30

31

oC

10 11 12 13 14 15

0

2

4

6

8

10

12

ppm

10 11 12 13 14 15

0

2

4

6

8

10

12

ppm

10 11 12 13 14 15

6.75

7.00

7.25

7.50

7.75

8.00

8.25

8.50

8.75

9.00

10 11 12 13 14 15

0

2

4

6

8

10

12

14

16

18

20

ppm

10 11 12 13 14 15

Surface Salinity

Surface Temp.

Surface DO

pH

Station Station

DOC

Bottom DO

Bottom Temp.

Bottom Salinity
Figure 16. Box-and-whisker plots of water quality variables by station in the landfill canals. 

0.0

1.0

2.0

3.0

4.0

5.0

6.0

ppm

10 11 12 13 14 15

0.00

0.05

0.10

0.15

0.20

0.25

0.30

ppb

10 11 12 13 14 15

NH4 NH3

0.00

0.02

0.04

0.06

0.08

0.10

ppm

10 11 12 13 14 15

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

ppm

10 11 12 13 14 15

0.00

0.01

0.02

0.03

ppm

10 11 12 13 14 15

0.00

0.01

0.02

0.03

ppm

10 11 12 13 14 15

0.0

0.2

0.4

0.6

0.8

1.0

ppm

10 11 12 13 14 15

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

ppm

10 11 12 13 14 15

NO2 NO3

SRP TP

TON Si(OH)4

Station Station
Station 11 

Figure 17. Comparison of landfill water quality variables from 1994 and current study. 

0

4

8

12

16

20

24

28

PSU

93-94 98-99

22

23

24

25

26

27

28

29

30

31

32

oC

93-94 98-99

1

2

3

4

5

6

7

8

mg/l

93-94 98-99

7.0

7.2

7.4

7.6

7.8

8.0

8.2

8.4

pH

93-94 98-99

0.0

0.2

0.4

0.6

0.8

1.0

ppm

93-94 98-99

0

5

10

15

20

25

30

35

40

ppb

93-94 98-99

0.0

0.1

0.2

0.3

0.4

0.5

ppm

93-94 98-99

0.000

0.010

0.020

0.030

0.040

0.050

ppm

93-94 98-99

Salinity

Dissolved Oxygen

Temperature

pH

Ammonium

Nitrate

Ammonia (NH3)

Soluble Reactive Phosphorus
Station 12 

Figure 18. Comparison of landfill water quality variables from 1994 and current study. 

0

4

8

12

16

20

24

28

PSU

93-94 98-99

22

23

24

25

26

27

28

29

30

31

32

oC

93-94 98-99

0

1

2

3

4

5

6

mg/l

93-94 98-99

6.8

7.0

7.2

7.4

7.6

7.8

8.0

8.2

8.4

93-94 98-99

0

5

10

15

20

25

30

35

ppm

93-94 98-99

0

100

200

300

400

500

ppb

93-94 98-99

0.0

0.1

0.2

0.3

0.4

0.5

ppm

93-94 98-99

0.00

0.01

0.02

0.03

0.04

0.05

ppm

93-94 98-99

Salinity

Dissolved Oxygen

Temperature

pH

Ammonium

Nitrate

Ammonia (NH3)

Soluble Reactive Phosphorus
Station 13 

Figure 19. Comparison of landfill water quality variables from 1994 and current study. 

0

2

4

6

8

10

12

14

16

18

20

22

24

26

PSU

93-94 98-99

22

23

24

25

26

27

28

29

30

31

32

oC

93-94 98-99

1

2

3

4

5

6

7

8

mg/l

93-94 98-99

7.0

7.2

7.4

7.6

7.8

8.0

8.2

8.4

pH

93-94 98-99

0.0

0.2

0.4

0.6

0.8

1.0

ppm

93-94 98-99

0

5

10

15

20

25

30

35

40

ppb

93-94 98-99

0.0

0.1

0.2

0.3

0.4

0.5

ppm

93-94 98-99

0.000

0.010

0.020

0.030

0.040

0.050

ppm

93-94 98-99

Salinity

Dissolved Oxygen

Temperature

pH

Ammonium

Nitrate

Ammonia (NH3)

Soluble Reactive Phosphorus
Station 15 

18

20

22

24

26

28

30

32

34

36

PSU

93-94 98-99

20

21

22

23

24

25

26

27

28

29

30

31

32

oC

93-94 98-99

4.0

5.0

6.0

7.0

8.0

9.0

mg/l

93-94 98-99

7.0

7.5

8.0

8.5

9.0

pH

93-94 98-99

0.0

0.1

0.2

0.3

0.4

0.5

ppm

93-94 98-99

0.0

1.0

2.0

3.0

4.0

5.0

6.0

7.0

ppb

93-94 98-99

0.0

0.1

0.2

0.3

0.4

0.5

ppm

93-94 98-99

0.000

0.010

0.020

0.030

0.040

0.050

ppm

93-94 98-99

Salinity

Dissolved Oxygen

Temperature

pH

Ammonium

Nitrate

Ammonia (NH3)

Soluble Reactive Phosphorus

Figure 20. Comparison of landfill water quality variables from 1994 and current study. 
Figure 21. Salinity data from combined Shoreline Ammonia Survey and April 1999 FIU 

Biscayne Bay water quality monitoring program. Note hypersaline conditions in the south below 

Military Canal. 

-80.40 -80.35 -80.30 -80.25 -80.20 -80.15 25.35

25.40

25.45

25.50

25.55

25.60

25.65

25.70

25.75

36

37

38

39

40

41

42

Salinity (ppt)

Goulds Canal

Mowry Canal

Military Canal

Cutler Channel

April 1999
Figure 22. Ammonium data from combined Shoreline Ammonia Survey and April 1999 FIU 

Biscayne Bay water quality monitoring program. Note strong source in and around the Goulds 

Canal/Black Point area. 

-80.40 -80.35 -80.30 -80.25 -80.20 -80.15 25.35

25.40

25.45

25.50

25.55

25.60

25.65

25.70

25.75

0.000

0.004

0.008

0.012

0.016

0.020

0.024

Ammonium (ppm)

Goulds Canal

Mowry Canal

Military Canal

Cutler Channel

April 1999
Figure 23. Unionized ammonia data from combined Shoreline Ammonia Survey and April 1999 

FIU Biscayne Bay water quality monitoring program. Note slightly higher concentrations around 

the Cutler Canal, Goulds Canal/Black Point area, and Fender Point. 

-80.40 -80.35 -80.30 -80.25 -80.20 -80.15 25.35

25.40

25.45

25.50

25.55

25.60

25.65

25.70

25.75

0.0

1.0

2.0

3.0

4.0

5.0

Ammonia (NH3-ppb)

Goulds Canal

Mowry Canal

Military Canal

Cutler Channel

April 1999
Figure 24. Nitrate data from combined Shoreline Ammonia Survey and April 1999 FIU 

Biscayne Bay water quality monitoring program. Note strong source from the Cutler Canal. 

-80.40 -80.35 -80.30 -80.25 -80.20 -80.15 25.35

25.40

25.45

25.50

25.55

25.60

25.65

25.70

25.75

0.000

0.002

0.004

0.006

0.008

0.010

Nitrate (ppm)

Goulds Canal

Mowry Canal

Military Canal

Cutler Channel

April 1999
Figure 25. Total Phosphorus data from combined Shoreline Ammonia Survey and April 1999 

FIU Biscayne Bay water quality monitoring program. Note elevated concentrations around 

Mangrove Key. 

-80.40 -80.35 -80.30 -80.25 -80.20 -80.15 25.35

25.40

25.45

25.50

25.55

25.60

25.65

25.70

25.75

0.000

0.010

0.020

0.030

0.040

0.050

Total Phosphorus (ppm)

Goulds Canal

Mowry Canal

Military Canal

Cutler Channel

April 1999
Figure 26. Total organic carbon data from combined Shoreline Ammonia Survey and April 1999 

FIU Biscayne Bay water quality monitoring program. Note elevated inshore concentrations 

occurring from Cutler Canal to Mowry Canal. 

-80.40 -80.35 -80.30 -80.25 -80.20 -80.15 25.35

25.40

25.45

25.50

25.55

25.60

25.65

25.70

25.75

0.0

1.0

2.0

3.0

4.0

5.0

6.0

7.0

8.0

9.0

10.0

Total Organic Carbon (ppm)

Goulds Canal

Mowry Canal

Military Canal

Cutler Channel

April 1999
Figure 27. Total organic nitrogen data from combined Shoreline Ammonia Survey and April 

1999 FIU Biscayne Bay water quality monitoring program. Note highest concentrations were 

found inshore between Goulds and Military Canals. 

-80.40 -80.35 -80.30 -80.25 -80.20 -80.15 25.35

25.40

25.45

25.50

25.55

25.60

25.65

25.70

25.75

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

Total Organic Nitrogen (ppm)

Goulds Canal

Mowry Canal

Military Canal

Cutler Channel

April 1999
Figure 28. Plot of NH4

+

 in water and sediments along Shoreline Nutrient Survey sites. 

Figure 29. Plot of TP in water and sediments along Shoreline Nutrient Survey sites. 

Ammonium

0.001

0.010

0.100

1.000

25.65 25.60 25.55 25.50 25.45 25.40 25.35

Latitude (N to S)

ppm

water column

sediment

Cutler Goulds Military Mowry

Total Phosphorus

0.000

0.001

0.010

0.100

1.000

25.65 25.60 25.55 25.50 25.45 25.40 25.35

Latitude (N to S)

ppm

water column

sediment

Cutler Goulds Military Mowry
Figure 30. Plot of plant species distribution along Shoreline Benthic Survey sites. 

Figure 31. Plot of Thalassia vs salinity along Shoreline Benthic Survey sites. 

0

1

2

3

4

5

6

25.65 25.60 25.55 25.50 25.45 25.40 25.35

Latitude (N to S)

Density

34

36

38

40

42

44

46

psu

Thalassia

Salinity

Cutler Goulds Military Mowry

Species Density

0

1

2

3

4

5

6

7

8

9

10

Thalassia

Latitude (N to S)

Braun-Blanquet

Unknown

Brown Algae

Acetabularia

Other Greens

Halodule

Red Algae

Penicillus

Thalassia

Cutler Goulds Military Mowry
Figure 32. Plot of Thalassia vs NH4

+

 along Shoreline Benthic Survey sites. 

0

1

2

3

4

5

6

25.65 25.60 25.55 25.50 25.45 25.40 25.35

Latitude (N to S)

Density

0.00

0.01

0.02

0.03

0.04

ppm

Thalassia

NH4

Cutler Goulds Military Mowry
Figure 33. Plots of water quality variables from the Mangrove Transect Surveys. Sites are 

distribution canal (DC) near Military Canal, adjacent mangrove fringe (CF), offshore CF (CBB), 

mangrove fringe near Mowry (TF), and offshore TF (TBB). 

0.0

0.2

0.4

0.6

0.8

1.0

1.2

ppm

CBB CF DC TBB TF

0.0

0.2

0.4

0.6

0.8

1.0

1.2

ppm

CBB CF DC TBB TF

0.00

0.05

0.10

0.15

0.20

ppm

CBB CF DC TBB TF

0.00

0.02

0.04

0.06

0.08

0.10

ppm

CBB CF DC TBB TF

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

μg/l

CBB CF DC TBB TF

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0

ppm

CBB CF DC TBB TF

NO2+NO3 NH4

TP SRP

Chl a TOC

Station Station