A view from the bridge: External and internal forces affecting the 

ambient water quality of the Florida Keys National Marine Sanctuary 

(FKNMS) 

Joseph N. Boyer1 and Ronald D. Jones1, 2

1

Southeast Environmental Research Center and 2Department of Biological Sciences, 

Florida International University, Miami, FL 33199 

boyerj@fiu.edu 

305-348-4076 (office) 

305-348-4096 (fax) 

Running Head: Water Quality in the FKNMS 

BOYER, J. N., AND R. D. JONES. (in press) A view from the bridge: External and internal forces 

affecting the ambient water quality of the Florida Keys National Marine Sanctuary, p. #-#. In

J. W. Porter and K. G. Porter (eds.), Linkages between ecosystems: the South Florida 

Hydroscape. St. Lucie Press. 
 2 

Acknowledgments 

 We thank all the field and laboratory technicians involved with this project including: J. 

Absten, O. Beceiro, N. Black, S. Bolanos, C. Covas, D. Diaz, T. Frankovich, B. Gilhooly, S. 

Kaczynski, E. Kotler, S. Perez, P. Sterling, F. Tam, and especially Pete Lorenzo. We want to 

thank the captains and crew of the R/V Bellows and R/V Suncoaster of the Florida Institute of 

Oceanography for their professional support of the monitoring program. We also appreciate the 

laboratory and lodging support supplied by the Florida Program of the National Underwater 

Research Center, UNC-Wilmington and FL-DEP Keys Marine Laboratory. This project was 

possible due to continued funding by the US-EPA under Agreement #X994621-94-0. Funding 

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

Florida Water Management District and Everglades National Park (SFWMD/NPS Coop. 

Agreement C-7919 and NPS/SERC Coop. Agreement 5280-2-9017). This is contribution #XX 

of the Southeast Environmental Research Center at Florida International University. 

 This publication is dedicated to the memory of Cristina Menendez. 
 3 

Introduction 

 The Florida Keys are a archipelago of sub-tropical islands of Pleistocene origin which extend 

in a NE to SW direction from Miami to Key West and out to the Dry Tortugas (Fig. 1). In 1990, 

President Bush signed into law the Florida Keys National Sanctuary and Protection Act 

(HR5909) which designated a boundary encompassing >2,800 square nautical miles of islands, 

coastal waters, and coral reef tract as the Florida Keys National Marine Sanctuary (FKNMS). 

The Comprehensive Management Plan (NOAA 1995) required the FKNMS to have a Water 

Quality Protection Plan (WQPP) thereafter developed by EPA and the State of Florida (EPA 

1995). The contract for the water quality monitoring component of the WQPP was subsequently 

awarded to the Southeast Environmental Research Program at Florida International University 

and the field sampling program began in March 1995. 

 The waters of the FKNMS are characterized by complex water circulation patterns over both 

spatial and temporal scales with much of this variability due to seasonal influence in regional 

circulation regimes. The FKNMS is directly influenced by the Florida Current, the Gulf of 

Mexico Loop Current, inshore currents of the SW Florida Shelf (Shelf), and by tidal exchange 

with both Florida Bay and Biscayne Bay. Advection from these external sources has significant 

effects on the physical, chemical, and biological composition of waters within the FKNMS, as 

does internal nutrient loading and freshwater runoff from the Keys themselves. Water quality of 

the FKNMS may be directly affected both by external nutrient transport and internal nutrient 

loading sources. Therefore, the geographical boundary of the FKNMS must not be thought of as 

enclosing a distinct ecosystem but rather as being one of political/regulatory definition. 

 Ongoing quarterly sampling of >200 stations in the FKNMS and Shelf, as well as monthly 

sampling of 100 stations in Florida Bay, Biscayne Bay, and the mangrove estuaries of the SW 

coast, has provided us with a unique opportunity to explore the spatial component of water 

quality variability. By stratifying the sampling stations according to depth, regional geography, 

distance from shore, proximity to tidal passes, and influence of Shelf waters we report some 

preliminary conclusions as to the relative importance of external vs. internal factors on the 

ambient water quality within the FKNMS. 

Methods 

Site Characteristics and Sampling Design 

 A spatial framework for FKNMS water quality management was proposed on the basis of 

geographical variation of regional circulation (Klein and Orlando 1994). The final 

implementation plan (EPA 1995) partitioned the FKNMS into 9 segments which was collapsed 

to 7 for routine sampling (Fig. 1). Station locations were developed using a stratified random 

design along onshore/offshore transects in Seg. 5, 7, and 9 or within EMAP grid cells in Seg. 1, 

2, 4, and 6. 

 Segment 1 (Tortugas) includes the Dry Tortugas National Park and surrounding waters and is 

most influenced by the Loop Current and Dry Tortugas Gyre. Segment 2 (Marquesas) includes 

the Marquesas Keys and a shallow sandy area between the Marquesas and Tortugas called the 

Quicksands; Segment 4 (Backcountry) contains the shallow, hard-bottomed waters of the 

gulfside Lower Keys. Segments 2 and 4 are both influenced by water moving south from the 

Shelf. Segment 6 can be considered as part of western Florida Bay. This area is referred to as 

the Sluiceway as it heavily influenced by transport from Florida Bay and the Shelf (Smith 1994). 
 4 

Segment 5 (Lower Keys), 7 (Middle Keys), and 9 (Upper Keys) include the inshore, Hawk 

Channel and reef tract of the Atlantic side of the Florida Keys. The Lower Keys are most 

influenced by cyclonic gyres spun off of the Florida Current, the Middle Keys by exchange with 

Florida Bay, while the Upper Keys are influenced by the Florida Current frontal eddies and to a 

certain extent by exchange with Biscayne Bay. All three oceanside segments are also influenced 

by wind and tidally driven lateral Hawk Channel transport (Pitts 1997). 

Field Sampling 

 The period of record of this study was from March 1995 to April 1998 and included 12 

quarterly sampling events. For each event, field measurements and grab samples were collected 

from 150 fixed stations within the FKNMS boundary (Fig. 1). Depth profiles of temperature 

(°C), salinity (psu), dissolved oxygen (DO, mg l-1), photosynthetically available radiation (PAR, 

μE m-2), in situ chlorophyll a specific fluorescence (FSU), optical backscatterance turbidity 

(OBS), depth as measured by pressure transducer (m), and density (σt, kg m-3) were measured by 

CTD casts (Seabird SBE 19). The CTD was equipped with internal RAM and operated in stand 

alone mode at a sampling rate of 0.5 sec. The vertical light attenuation coefficient (Kd, m

-1) was 

calculated at 0.5 m intervals from PAR and depth using the standard exponential equation (Kirk 

1994) and averaged over the station depth. This was necessary due to periodic occurrence of 

optically distinct layers within the water column. During these events, Kd was reported for the 

upper layer. 

 In the Backcountry area (Seg. 4, Fig. 1) where it was too shallow to use a CTD, surface 

salinity and temperature were measured using a combination salinity-conductivity-temperature 

probe (Orion model 140). DO was measured using an oxygen electrode (Orion model 840) 

corrected for salinity and temperature. PAR was measured using a Li-Cor irradiance meter 

equipped with two 4π spherical sensors (LI-193SB) separated by 0.5 m in depth and oriented at 

90° to each other. The light meter measured instantaneous difference between sensors which was 

then used to calculate Kd from in-air surface irradiance. 

 Water was collected from ~0.25 m below the surface and at ~1 m from the bottom with a 

teflon-lined Niskin bottle (General Oceanics) except in the Backcountry where it was collected 

directly into sample bottles. 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. The wet filters used for chlorophyll a (Chl a) analysis, were placed in 1.8 ml 

plastic centrifuge tubes to which 1.5 ml of 90 % acetone/water was added (Strickland and 

Parsons 1972). 

 Unfiltered samples were kept at ambient temperature in the dark during transport to the 

laboratory. During shipboard collection in the Tortugas/Marquesas and overnight stays in the 

Keys, unfiltered samples were analyzed for alkaline phosphatase activity (APA) and turbidity 

(see Analytical) prior to refrigeration. Filtered samples and filters were kept on ice in the dark 

during transport. During shipboard collection in the Tortugas/Marquesas and overnight stays in 

the lower Keys, filtrates and filters were frozen until analysis. 

Laboratory Analysis 
 5 

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

total phosphorus (TP), silicate (Si(OH)4), alkaline phosphatase activity (APA), and turbidity 

(NTU). TOC was measured by direct injection onto hot platinum catalyst in a Shimadzu TOC5000 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). Si(OH)4 was measured using the 

molybdosilicate method (Strickland and Parsons 1972). The APA assay measures the activity of 

alkaline phosphatase, an enzyme used by bacteria to mineralize orthophosphate from organic 

compounds. The assay is performed by adding a known concentration of an organic phosphate 

compound (methylfluorescein phosphate) to an unfiltered water sample. AP in the water sample 

cleaves the orthophosphate, leaving methylfluorescein, a highly fluorescent compound. 

Fluorescence at initial and after 2 hr incubation were measured using a Gilford Fluoro IV 

Spectrofluorometer (excitation = 430 nm, emission = 507 nm) and subtracted to give APA in μM 

h-1 (Jones 1996). 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). 

Filters for Chl a content (μg l-1) were allowed to extract for a minimum of 2 days at -20°C before 

analysis. Extracts were analyzed using a Gilford Fluoro IV Spectrofluorometer (excitation = 435 

nm, emission = 667 nm). All analyses were completed within 1 month after collection in 

accordance to SERC laboratory quality control guidelines. 

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

(NO3

-

) 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 μM unless 

noted. All elemental ratios discussed were calculated on a molar basis. Percent DO saturation 

(DOsat as %) was calculated using the equations of Garcia and Gordon (1992). 

Statistical Analysis 

 Stations were grouped four different ways for statistical analysis: by surface or bottom 

samples, surface by segment, surface by transect distance, and surface by shore type. These 

groupings were subjectively defined using best available knowledge in an effort to provide 

information as to source, transport, and fate of water quality components. For the first grouping, 

stations were selected as being >3 m depth where both surface and bottom samples were 

collected and stratified by depth. The second grouping included surface samples stratified by 

segment (Fig. 1) in accordance with the implementation plan (EPA 1995). The third grouping 

consisted of those surface stations situated on ocean-side transects being aggregated according to 

their distance from shore: Alongshore, Hawk Channel, or Reef Tract. In addition, we initiated a 

transect of stations in the Tortugas off Loggerhead Key to serve as a reference. Since sampling at 

these locations in the Tortugas were only recently set up to address this question, the data is more 

sparse. Also there are only two “channel” stations in the Tortugas which makes the data more 

susceptible to outlier conditions. 

 One of the concerns of this program is to determine the contribution of water movement 

through the passes of the Keys to the water quality of the reef. To this end we decided to 

characterize the last grouping of transects as to shore type: those that are adjacent to land off 
 6 

Biscayne National Park off Old Rhodes Key, Elliot Key and the Safety Valve (BISC), those that 

abut land in Key Largo, Middle, and Lower Keys (LAND), and those transects which are aligned 

along an open channel or pass through the Keys (PASS). These grouping strategies may be 

changed when enough data is collected (ca. 5-7 yr) to be analyzed using a statistically objective, 

multivariate approach as has been done previously for Florida Bay and Ten Thousand Islands 

(Boyer et al. 1997; Boyer and Jones 1998). 

 Typical water quality variables are usually skewed to the left resulting in non-normal 

distributions. Therefore it is more appropriate to use the median as the measure of central 

tendency. Data distributions of selected water quality variables are reported as box-and-whiskers 

plots. The box-and-whisker plot is a powerful statistic as it shows the median, range, the data 

distribution as well as serving as a graphical, nonparametric ANOVA. The center 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), and the ends of the whiskers are the 5th and 95th percentiles. The notch in 

the box is the 95% confidence interval of the median. When notches between boxes do not 

overlap, the medians are considered significantly different. Outliers (<5th and >95th percentiles) 

were excluded from the graphs to reduce visual compression. Differences in variables were also 

tested between groups using the Wilcoxon Ranked Sign test (comparable to t-test) and among 

groups by the Kruskall-Wallace test (ANOVA) with significance set at P<0.05. 

 In an effort to elucidate the contribution of external factors to the water quality of the 

FKNMS and to visualize gradients in water quality over the region, we combined data from other 

portions of our water quality monitoring network: Florida Bay, Biscayne Bay, Whitewater Bay, 

Ten Thousand Islands, and the Shelf (Fig. 1). Data from these 153 additional stations was 

collected during the same month as the FKNMS surveys and analyzed by SERC personnel using 

similar methodology and quality control as previously described. Spatial contour maps of 

median water quality variables (of 12 surveys) were generated in SURFER (Golden Software) 

using the Kriging algorithm. 

Results 

Overall Water Quality 

 Summary statistics for all surface water quality variables including data from all 12 sampling 

events and all stations for the period of record (Table 1) are shown as median value, minimum 

value, maximum value, and number of samples measured. Overall, the region was warm and 

euhaline with a median temperature of 26.7°C and salinity of 36.2 psu. The median DO was 6.2 

mg l-1, or ~93 % DOsat. On this coarse scale, the FKNMS exhibited very good water quality with 

median NO3

-

, NH4

+

, and TP concentrations of 0.10, 0.32, and 0.18 μM, respectively. NH4

+

 was 

the dominant DIN species in almost all of the samples (~70 %). DIN comprised a small fraction 

(4 %) of the TN pool with TON making up the bulk (11.4 μM). SRP concentrations were very 

low (median 0.01 μM) and comprised only 6 % of the TP pool. Chl a concentrations were very 

low overall, 0.25 μg l-1, but ranged from 0.01 to 6.8 μg l-1. Median turbidity was low (0.6 NTU) 

as reflected in a low Kd (0.206 m-1). This resulted in a median photic depth (to 1 % incident 

PAR) of ~22 m. Molar ratios of N to P suggested a general P limitation of the water column; 

median TN:TP = 67 and median DIN:SRP = 49. 

Stations Grouped by Depth
 7 

 Some general differences were observed for those stations >3 m depth where both surface 

and bottom concentrations were measured. Temperature, DO, TOC, and TON were significantly 

higher at the surface while salinity, NO3

-

, NO2

-

, NH4

+

, TP, and turbidity were significantly higher 

in bottom waters. There were no significant differences in SRP, APA, or Si(OH)4 with depth. 

Stations Grouped By Segment 

 NO3

-

 was highest in the Backcountry (0.18 μM) followed by the Lower and Middle Keys. 

Interestingly, NO3

-

 concentrations in the Sluiceway (0.08 μM) were not significantly different 

than the Upper Keys, Tortugas, or Marquesas. Median NO2

-

 concentrations in the Tortugas and 

Marquesas (0.03 μM) were significantly lower than for the other Keys segments. NH4

+

 was 

highest in the Backcountry (0.46 μM) and lowest in the Tortugas, Marquesas, and Upper Keys 

(~0.25 μM). The Middle Keys had the most variability in DIN for any of the ocean-side 

segments. 

 TP was highest in the Backcountry and Sluiceway (~0.21 μM) and lowest in the Upper Keys 

(0.15 μM) with the remaining segments being intermediate (Fig. 2). SRP was very low (~0.01 

μM) for all areas but was slightly elevated and most variable in the Marquesas and Backcountry. 

Median Si(OH)4 concentrations were highest in the Sluiceway (4.9 μM), lowest in the Tortugas, 

Marquesas, and Upper Keys (~0.45 μM), and intermediate in the Backcountry, Lower, and 

Middle Keys (~1.4 μM). Consistently higher Chl a concentrations were observed in the 

Marquesas (0.36 μg l-1) than for any other area of the FKNMS (Fig. 2). Lowest Chl a

concentrations were found in the Upper Keys (0.20 μg l-1). 

 The organic C and N pools as well as APA showed remarkable similarity in relative 

concentration among segments (Fig. 3). Highest TOC (~260 μM), TON (~15.5 μM), and APA 

(~0.08 μM h-1) were observed in the Backcountry and Sluiceway which declined SW towards the 

Tortugas and NE towards the Upper Keys. Median DOsat was relatively similar among segments 

but was significantly higher and more variable in the Backcountry and Sluiceway (~95 %). This 

result would not have been evident had we only reported DO in mg l-1 as it was not significant 

across segments. 

 Salinity was comparable for most segments but was slightly lower in the Sluiceway (Fig. 3). 

Salinity in the Sluiceway and Backcountry were highly variable and precluded any statistical 

discrimination from the other segments. Turbidity was highest in the Backcountry (1.0 NTU), 

Sluiceway (0.85 NTU), and Marquesas (0.83 NTU) with lowest turbidity occurring in the 

Tortugas segment (0.35 NTU, Fig. 3). The shallow Quicksands area in the Marquesas probably 

accounted for the elevated turbidity in this segment. The Middle Keys showed high variability in 

turbidity although the overall median was low. 

 The Tortugas, Marquesas, and Lower Keys had significantly higher water temperature 

(~27.3°C) than the other segments (Fig. 4). Light attenuation showed a similar pattern as 

turbidity with highest Kd in Sluiceway (0.36 m-1) and Backcountry stations (0.31 m-1) and lowest 

Kd in the Tortugas (0.12 m-1). This works out to respective median photic depths of 13, 15, and 

38 m. Median TN:TP ratios in the Tortugas (55) and Marquesas (52) were significantly lower 

than in the other segments (Fig. 4). Much of this difference was due to decreased TON 

concentrations in these areas rather than increased in TP. Lowest DIN:SRP ratios were found in 

the Marquesas (29) followed by the Tortugas (39). Decreased DIN as well as elevated SRP in 

the Marquesas relative to the Tortugas was responsible for these differences. 
 8 

Stations Grouped By Distance along Transect 

 Median concentrations of NO3

-

 in the Middle, and Lower Keys were significantly higher in 

Alongshore stations than those of Hawk Channel and Reef Tract (Fig. 5). Alongshore NO3

-

 in 

the Upper Keys and Tortugas (~0.1 μM) was not nearly as high as found in the Middle and 

Lower Keys (~2.5 μM). NO3

-

concentrations on the Reef Tract and offshore in the Tortugas, 

Upper, and Middle Keys were comparable (~0.05 μM) and were all significantly lower than for 

the Lower Keys. NH4

+

 concentrations followed similar trends as NO3

-

 being higher in 

Alongshore stations in the Middle and Lower Keys and declined with distance offshore (Fig. 5). 

Alongshore NH4

+

 was highest in the Middle Keys (~0.5 μM). No significant differences in NH4

+

was seen among Hawk Channel, Reef Tract, and Tortugas groups (~0.3 μM). 

 Alongshore TP concentrations (~0.18 μM) were significantly higher than the Reef Tract only 

in the Lower Keys (Fig. 5). The Middle Keys and Tortugas showed no offshore trend while the 

Upper Keys showed a slight increasing trend in TP from shore to reef. TP concentrations in the 

Tortugas, Lower, and Middle Keys were comparable (~0.18 μM) while the Upper Keys were 

lowest overall (~0.16 μM). The major trends in TP were mirrored by SRP but were not 

statistically significant. Median Si(OH)4 concentrations dropped dramatically with distance 

offshore in the Middle Keys (Fig. 5). In the Lower Keys, Si(OH)4 was significantly lower only in 

the Reef Tract stations. There was no difference in Si(OH)4 concentrations in the Upper Keys or 

Tortugas transects. Alongshore Si(OH)4 concentrations were highest in the Middle Keys (~3 

μM) while Reef Tract concentrations were highest in the Lower Keys (~0.5 μM). 

 There was no significant trend in Chl a with distance from land in the Lower Keys (Fig. 6), 

although there was a slight decline in the Middle Keys and a small increase in the Upper Keys. 

Chl a in the Offshore Tortugas sites was significantly lower than Alongshore and Channel sites 

and was comparable to levels in the Upper Keys (0.2 μg l-1). TOC in the Lower, Middle, and 

Upper Keys was elevated Alongshore and declined sequentially through Hawk Channel to the 

Reef Tract (Fig. 6). There was no significant difference in TOC within Tortugas groups (~170 

μM) and was similar to Reef Tract concentrations in the Keys. Highest TOC in Alongshore 

stations occurred in the Middle Keys (~250 μM). TON concentrations exhibited similar patterns 

as TOC (data not shown). 

 Turbidity in all segments declined significantly with distance from land (Fig. 6). All Reef 

Tract and Offshore Tortugas sites had comparably low turbidity levels (~0.2 NTU). Highest 

Alongshore turbidity was found in the Middle Keys (1.3 NTU). No significant differences in 

Alongshore turbidity in the Tortugas, Lower, and Upper Keys were observed (~0.6 NTU). 

Trends in median salinity with distance offshore were small; trends in salinity variability were 

large (Fig. 6). Salinity from Alongshore to Reef Tract increased significantly in the Upper Keys 

whereas in the Lower Keys, salinity actually decreased offshore. No significant change in 

salinity was observed along Middle Keys, Marquesas, or Tortugas transects. In all segments, 

Alongshore salinities were much more variable than those of Reef Tract and Offshore. Reef 

Tract and Tortugas Offshore salinities were not significantly different, therefore, Alongshore 

salinity in the Lower Keys was higher than local seawater values while Alongshore salinity in the 

Upper Keys was depressed relative to local seawater values. 

Stations Grouped By Shore Type 

 Ocean-side transects showed marked differences in water quality when grouped by shore type 

(Fig. 7). Transects situated on open channels (Pass) through the Keys were elevated in NO3

-

, 
 9 

NH4

+

, TP, Si(OH)4, Chl a, TOC, and turbidity relative to those against the island chain (Land). 

Both salinity and temperature were significantly lower in Pass transects than for Land. Although 

these differences were statistically significant, the absolute differences were very small being 

only fractional. We also found that these effects diminished rapidly with distance offshore (data 

not shown). Interestingly, those transects located along Biscayne National Park (Old Rhodes 

Key, Elliot Key, the Safety Valve) were lowest of all for NO3

-

, NH4

+

, TP, Si(OH)4, and Chl a. 

Discussion 

 Distinguishing internal from external sources of nutrients in the FKNMS is a difficult task. 

The finer discrimination of internal sources into natural and anthropogenic inputs is even more 

difficult but most important as anthropogenic inputs may be regulated and possibly controlled by 

management activities. Advective transport of nutrients through the FKNMS was not measured 

by the existing fixed sampling plan. However, nutrient distribution patterns may be compared to 

the regional circulation regimes in an effort to visualize the contribution of external sources and 

advective transport to internal water quality of the FKNMS. 

 Circulation in coastal South Florida is dominated by regional currents such as the Loop 

Current, Florida Current, and Tortugas Gyre and by local transport via Hawk Channel and alongshore Shelf movements (Klein and Orlando 1994). Regional currents may influence water 

quality over large areas by the advection of external surface water masses into and through the 

FKNMS (Lee et al. 1994) and by the intrusion of deep offshore ocean waters onto the reef tract 

as internal bores (Leichter et al. 1996). Local currents become more important in the mixing and 

transport of freshwater and nutrients from terrestrial sources (Smith 1994; Pitts 1997). 

 Spatial patterns of salinity in coastal South Florida show these major sources of freshwater to 

have more than just local impacts (Fig. 8). In Biscayne Bay, freshwater is released through the 

canal system operated by SFWMD; the impact is clearly seen to affect northern Key Largo by 

causing a depression in median salinity coupled with high variability in alongshore sites (Fig. 6 

and 7). Freshwater entering NE Florida Bay via overland flow from Taylor Slough and C-111 

basin in ENP can be seen to mix in a SW direction. The extent of influence of freshwater from 

Florida Bay on alongshore salinity in the Keys is less than that of Biscayne Bay but it is more 

episodic. Transport of low salinity water from Florida Bay does not affect the Middle Keys sites 

enough to depress the median salinity in this region but is manifested as increased variability 

(Fig. 6). On the west coast, the large influence of the Shark River Slough, which drains the bulk 

of the Everglades and exits through the Whitewater Bay - Ten Thousand Islands mangrove 

complex, is clearly seen as impacting the Shelf waters (Fig. 8). The mixing of Shelf waters with 

the Gulf of Mexico produces a salinity gradient in a SW direction which extends out to Key 

West. This freshwater source does not seem to impact the Backcountry because of its shallow 

nature but instead follows a trajectory of entering western Florida Bay and exiting out through 

the channels in the Middle Keys (Smith 1994). This net transport of lower salinity water from 

mainland to reef in open channels through the Keys is observed more so as an increase in the 

range and variability of salinity than as a large depression in salinity (Fig. 7). 

 In addition to surface currents there is evidence that internal tidal bores regularly impact the 

Key Largo reef tract (Leichter et al. 1996). Internal bores are episodes of higher density, deep 

water intrusion onto the shallower shelf or reef tract. Depending on their energy, internal tidal 

bores can promote stratification of the water column or cause complete vertical mixing as a 
 10 

breaking internal wave of subthermocline water. To determine the extent of stratification we 

calculated the difference between surface and bottom density, delta sigma-t (∆σt), where positive 

values denoted greater density of bottom water relative to the surface. The resulting graph of ∆σt

(Fig. 9), shows that the SW area of the Tortugas segment tends to experience the greatest 

frequency of stratification events. The decreased temperature and increased salinity in bottom 

waters from intrusion of deeper denser oceanic waters to this region may also account for 

increases in NO3

-

, TP, and SRP in these bottom waters as well. For example, in April 1998 a 

mass of colder, nutrient laden water from the Gulf of Mexico moved up onto the Tortugas reefs 

and fueled a large benthic macroalgae bloom (J. Porter, pers. comm.). This event was observed 

throughout most of the eastern Gulf as far north as Pensacola (NOAA ????). At the two most 

SW stations (Table 2), temperatures dropped ~4°C, NO3

-

 increased 3 orders of magnitude, SRP 

and Si(OH)4 increased by a factor of 100, while TP, turbidity, and in vivo Chl a specific 

fluorescence (measured via CTD) all doubled. As there was only a small increase in NH4

+

during this event we believe the general case of elevated NH4

+

 and turbidity found in bottom 

waters throughout the FKNMS is most probably due to benthic flux and resuspension and not to 

subthermocline advection. 

 Surface Si(OH)4 concentrations exhibited a pattern similar to salinity (Fig. 10). The source 

of Si(OH)4 in this geologic area of carbonate rock and sediments is from siliceous periphyton 

(diatoms) growing in the Shark River Slough, Taylor Slough, and C-111 basin watersheds. 

Unlike the Mississippi River plume with Chl a concentrations of 76 μg l-1 (Nelson and Dortch 

1996), phytoplankton biomass on the Shelf (1-2 μg l-1 Chl a) was not sufficient to account for 

the depletion of Si(OH)4 in this area. Therefore, Si(OH)4 concentrations on the Shelf were 

rapidly depleted by mixing alone allowing Si(OH)4 to be used as a semi-conservative tracer of 

freshwater in this system (Ryther et al. 1967; Moore et al. 1986). Unlike Florida Bay and the 

west coast, there was very little Si(OH)4 loading to southern Biscayne Bay, mostly because the 

source of freshwater to this system is from canals which drain agricultural and urban areas of 

Dade County. 

 In the Lower and Middle Keys, it is clear that the source of Si(OH)4 to the nearshore Atlantic 

waters is through the Sluiceway and Backcountry. Si(OH)4 concentrations near the coast were 

elevated relative to the reef tract with much higher concentrations occurring in the Lower and 

Middle Keys than the Upper Keys (Fig. 5). There is an interesting peak in Si(OH)4 concentration 

in an area of the Sluiceway which is densely covered with the seagrass, Syringodium (Fourqurean 

this issue). We are unsure as to the source but postulate that it may be due to benthic flux.

 Visualization of spatial patterns of NO3

-

 concentration over South Florida waters provide an 

extended view of source gradients over the region (Fig. 11). Biscayne Bay, Florida Bay, and the 

Shark River area of the west coast exhibited high NO3

-

 concentrations relative to the FKNMS 

and Shelf. Elevated NO3

-

 in Biscayne Bay is the result of loading from both the canal drainage 

system and from inshore groundwater (Alleman et al. 1995, Meeder ????). The source of NO3

-

to Florida Bay is the Taylor Slough and C-111 basin (Boyer and Jones, 1999; Rudnick et al., 

1999) while the Shark River Slough impacts the west coast mangrove rivers and out onto the 

Shelf (Rudnick et al., 1999). The oceanside transects off Biscayne Bay in Seg. 9 exhibited the 

lowest NO3

-

 alongshore compared to the Middle and Lower Keys. A similar pattern was 

observed in a previous transect survey from these areas (Szmant and Forrester 1996). They also 

showed an inshore elevation of NO3

-

 relative to Hawk Channel and the reef tract which is also 

demonstrated in our analysis (Fig. 5). Interestingly, NO3

-

 concentrations in all stations in the 
 11 

Tortugas transect were similar to those of reef tract sites in the mainland Keys; there was no 

inshore elevation of NO3

-

 on the transect off uninhabited Loggerhead Key. 

 Figure 10 also shows that a distinct intensification of NO3

-

 occurs in the Backcountry region. 

Part of this increase may due to a local sources of NO3

-

, i.e. septic systems and stormwater runoff 

around Big Pine Key (Lapointe and Clark 1992). However, there is another area, the Snipe Keys, 

that exhibits high NO3

-

 which is uninhabited by man. This rules out the premise of septic 

systems being the only source of NO3

-

 in this area. It is important to note that the Backcountry 

area is very shallow (~0.5 m) and hydraulically isolated from the Shelf and Atlantic which results 

in its having a relatively long water residence time. Elevated NO3

-

 concentrations may be 

partially due to simple evaporative concentration as is seen in salinity (Fig. 8). 

 Total dissolved NH4

+

 concentrations were distributed in a similar manner as NO3

-

 with 

highest concentrations occurring in Florida Bay, the Ten Thousand Islands, and the Backcountry 

(data not shown). NH4

+

 concentrations were very low in Biscayne Bay because it is not a major 

component of loading from the canal drainage system. NH4

+

 also showed similarities with NO3

-

 

in its spatial distribution, being lowest in the Upper Keys and highest inshore relative to offshore. 

There was no alongshore elevation of NH4

+

 concentrations in the Tortugas where levels were 

similar to those of reef tract sites in the mainland Keys. That the least developed portion of the 

Upper Keys in Biscayne National Park and uninhabited Loggerhead Key (Tortugas) exhibited 

lowest NO3

-

 and NH4

+

 concentrations is evidence of a local anthropogenic source for both of 

these variables along the ocean side of the Upper, Middle, and Lower Keys. This pattern of 

decline implies an onshore source which is diluted with distance from land by low nutrient 

Atlantic Ocean waters. 

 Elevated DIN concentrations in the Backcountry, on the other hand, are not so easily 

explained. We postulate that the high concentrations found there are due to a combination of 

anthropogenic loading, physical entrapment, and benthic N2 fixation. The relative contribution 

of these potential sources is unknown. Lapointe and Matzie (1996) have shown that stormwater 

and septic systems are responsible for increased DIN loading in and around Big Pine Key. The 

effect of increased water residence time in DIN concentration is probably small. Salinities in this 

area were only 1-2 psu higher than local seawater which resulted in a concentration effect of only 

5-6%. Benthic N2 fixation may potentially be very important in the N budget of the Backcountry. 

Measured rates of N2 fixation in a Thalassia bed in Biscayne Bay, having very similar physical 

and chemical conditions, were 540 μmol N m-2 d-1 (Capone and Taylor 1980). Without the plant 

community N demand, one day of N2 fixation has the potential to generate a water column 

concentration of >1 μM NH4

+

 (0.5 m deep). Much of this NH4

+

 is probably nitrified and may 

help account for the elevated NO3

-

 concentrations observed in this area as well. Clearly, N2

fixation may be a significant component of the N budget in the Backcountry and that it may be a 

exported as DIN to the FKNMS in general. 

 Spatial patterns in TP in South Florida coastal waters were strongly driven by the west coast 

outputs (Fig 12). A declining gradient in TP extended from the inshore waters of Whitewater 

Bay - Ten Thousand Islands mangrove complex out onto the Shelf and Tortugas. A declining 

gradient also extended from north central Florida Bay to the Middle Keys. Brand (1997) has 

postulated that groundwater from a subterranean Miocene quartz sand channel, "the river of 

sand", containing high levels of phosphorus is the source of TP in this region. However, no 

evidence of this source exists to date and the data from Florida Bay does not indicate a 

subterranean source either (Boyer and Jones unpublished data). A very small TP gradient was 
 12 

seen NE Florida Bay signifying that Taylor Slough and the C-111 basin contribute little TP to the 

system. Finally, there was no evidence of a significant terrestrial source of TP to Biscayne Bay. 

 In the Keys, there was evidence of elevated TP in alongshore stations of the Middle and 

Lower Keys but the differences were very small (Fig. 5). The Upper Keys actually showed 

higher TP concentrations on the reef tract than inshore implying an offshore source. 

Interestingly, the Tortugas area had higher TP concentrations than the Upper Keys as a result of 

Shelf water advection. 

 In South Florida coastal waters, very little of TP is found in the inorganic form (SRP - PO4

-

); 

most is organic P (TOP). The distribution of SRP on the west coast and Shelf was similar to that 

of TP with the general gradient from the west coast to Tortugas remaining (Fig 13). However, 

the SRP distribution was distinctly different from that of TP in Florida Bay, Whitewater Bay, and 

Biscayne Bay. In central Florida Bay the N-S gradient previously observed for TP was highly 

diminished for SRP indicating that almost all the TP in central Florida Bay was in the form of 

TOP. It is unlikely that the source of TOP to this region is from overland flow or groundwater as 

this is also the region that expresses highest salinity. Alternately, we hypothesize that the 

presence of the Flamingo channel, running parallel to the southern coastline of Cape Sable, acts 

as a tidal conduit for episodic advection of inshore Shelf water to enter north central Florida Bay. 

Subsequent trapping and evaporation then may act to concentrate TOP in this region. The second 

difference in P distributions was that there was a significant SRP gradient present in NE Florida 

Bay that was not observed for TP. The sources of SRP to this area are the Taylor Slough and C111 basin (W. Walker per. communication; Boyer and Jones, 1999; Rudnick et al., 1999). 

 Whitewater Bay displayed an east-west gradient in SRP concentrations which increased with 

salinity leading us to conclude that the freshwater inputs from the Everglades were not a source 

of SRP to this area. Finally, there was evidence of a significant onshore-offshore SRP gradient in 

southern Biscayne Bay; most probably as a direct result of canal loading and groundwater 

seepage to this region (A. Lietz personal communication; Meeder et al. 1997). 

 Concentrations of TOC (Fig. 14) and TON (not shown) are remarkably similar in pattern of 

distribution across the South Florida coastal hydroscape. The decreasing gradient from west coast 

to Tortugas was very similar to that of TP. A steep gradient with distance from land was 

observed in Biscayne Bay. Both these gradients were due to terrestrial loading. On the west 

coast, the source of TOC and TON was from the mangrove forests. Our data from this area 

shows that concentrations of TOC and TON increased from Everglades headwaters through the 

mangrove zone and then decrease with distance offshore. In Biscayne Bay, much of the TOC 

and TON is from agricultural land use. The high concentrations of TOC and TON found in 

Florida Bay were due to a combination of terrestrial loading (Boyer and Jones, 1999), in situ 

production by seagrass and phytoplankton, and evaporative concentration (Fourqurean et al. 

1993). 

 Advection of Shelf and Florida Bay waters through the Sluiceway and passes accounted for 

this region and the inshore area of the Middle Keys as having highest TOC and TON of the 

FKNMS (Fig. 7). Strong offshore gradients in TOC and TON existed for all mainland Keys 

segments (Fig. 6) but not for the Tortugas transect. Part of this difference may be explained by 

the absence of mangroves in the single Tortugas transect. The higher concentrations of TOC and 

TON in the inshore waters of the Keys then implies a terrestrial source rather than simply benthic 

production and sediment resuspension. Main Keys reef tract concentrations of TOC and TON 

were similar to those found in the Tortugas. 
 13 

 Much emphasis has been placed on assessing the impact of episodic phytoplankton blooms in 

Florida Bay on the offshore reef tract environment. Spatial patterns of Chl a concentrations (Fig. 

15) showed that NW Florida Bay, Whitewater Bay, and the Ten Thousand Islands exhibited high 

levels of Chl a relative to Biscayne Bay, Shelf, and FKNMS. The highest Chl a concentrations 

were found in west coast mangrove estuaries (up to 45 μg l-1 in Alligator Bay, TTI). Chl a is also 

routinely high (~2 μg l-1) in NW Florida Bay along the channel connecting the Shelf to Flamingo, 

ENP. It is interesting that Chl a concentrations are higher in the Marquesas (0.36 μg l-1) than in 

other areas of the FKNMS (Fig. 2). When examined in context with the whole South Florida 

ecosystem, it is obvious that the Marquesas zone should be considered a continuum of the Shelf 

rather than a separate management entity. This shallow sandy area (often called the Quicksands) 

acts as a physical mixing zone between the Shelf and the Atlantic Ocean and is a highly 

productive area for other biota as well as it encompasses the historical Tortugas shrimping 

grounds. A Chl a concentration of 1 μg l-1 in the water column of a reef tract is considered a 

problem as it indicates potential of eutrophication. On the other hand, a similar Chl a level in the 

Quicksands indicates a productive shrimp fishery. 

 The oceanside transects in the Upper Keys (Seg. 9) exhibited the lowest overall Chl a

concentrations of any zone in the FKNMS. Ocean transects showed a slight increase in Chl a on 

the reef tract in this area (Fig. 6). Transects off the Middle and Lower Keys showed that a drop 

in Chl a occurred only in the reef tract sites; there was no linear decline with distance from shore 

(data not shown). alongshore compared to the Middle and Lower Keys. Interestingly, Chl a

concentrations in the Tortugas transect showed a similar pattern as the mainland Keys. Inshore 

and Hawk Channel Chl a concentrations among Middle Keys, Lower Keys and Tortugas sites 

were not significantly different. As inshore Chl a concentrations in the Tortugas were similar to 

those in the Middle and Lower Keys, we see no evidence of phytoplankton bloom transport from 

Florida Bay under this type of sampling design. There was however some slight evidence of 

increased Chl a in those stations situated along the major passes in the Keys relative to those 

abutting land (Fig. 7). The differences between these two groupings were very small (0.25 vs. 

0.20 μg l-1). 

 Along with P concentration, turbidity is probably the second most important determinant of 

local ecosystem health. The fine, low density carbonate sediments in this area are easily 

resuspended, rapidly transported, and have high light scattering potential per gram of material. 

High water column turbidity and transport directly affects filter feeding organisms by clogging 

their feeding apparatus and by increasing local sedimentation rate. Sustained high turbidity of 

the water column indirectly affects benthic community structure by decreasing light penetration, 

promoting seagrasses extinction. Large scale observations of turbidity clearly show patterns of 

onshore-offshore gradients which extend out onto the Shelf to the Marquesas (Fig. 16). In the 

last seven years, turbidities in Florida Bay have increased dramatically in the NE and central 

regions (Boyer et al. 1998) potentially as a consequence of destabilization of the sediment from 

seagrass die-off (Robblee et al. 1991). 

 Strong turbidity gradients were observed for all Keys transects (Fig. 6) but reef tract levels 

were remarkably similar regardless of inshore levels. High alongshore turbidity is most probably 

due to the shallow water column being easily resuspended by wind and wave action. Inshore 

stations in the Middle Keys had higher turbidity than other segments. Transects aligned with 

major passes had slightly greater turbidity than those against land but the difference was not 

statistically significant (Fig. 7). Light extinction (Kd) was highest alongshore and improved with 
 14 

distance from land (data not shown). This trend was expected as light extinction is directly 

related to the turbidity of the water. 

 Using the DIN:SRP ratio is a relatively simple method of determining phytoplankton nutrient 

limitation status of the water column (Redfield 1967). Most of the South Florida hydroscape was 

shown to have DIN:SRP values >> 16:1, indicating the potential for phytoplankton to be limited 

by P at these sites (Fig. 17). The bulk of Florida Bay and both southern and northern Biscayne 

Bay were severely P limited, mostly as a result of high DIN concentrations. All of the FKNMS is 

routinely P limited using this metric. Interestingly, the Marquesas/Quicksands area was the least 

P limited of all zones and exhibited a significant regression between SRP and Chl a. Only in the 

northern Ten Thousand Islands and Shelf did N become the limiting nutrient. The south-north 

shift from P to N limitation observed in the west coast estuaries has been ascribed to changes in 

landuse and bedrock geochemistry of the watersheds (Boyer and Jones 1998). The west coast 

south of 25.4 N latitude is influenced by overland freshwater flow from the Everglades and Shark 

River Slough having very low P concentrations relative to N. Above 25.7 N latitude the bedrock 

geology of the watershed changes from carbonate to silicate based and landuse changes from 

relatively undeveloped wetland (Big Cypress Basin) to a highly urban/agricultural mix (Naples, 

FL). 

 The large scale of this monitoring program has allowed us to assemble a much more holistic 

view of broad physical/chemical/biological interactions occurring over the South Florida 

hydroscape. Much information has been gained by inference from this type of data collection 

program: major nutrient sources have be confirmed, relative differences in geographical 

determinants of water quality have been demonstrated, and large scale transport via circulation 

pathways have been elucidated. In addition we have shown the importance of looking "outside 

the box" for questions asked within. Rather than thinking of water quality monitoring as being a 

static, non-scientific pursuit it should be viewed as a tool for answering management questions 

and developing new scientific hypotheses. One of the more important management questions to 

be answered is "Is the water quality better or worse than it used to be?" As it stands, this 

monitoring program based on quarterly sample intervals may require up to 10 years before small 

trends may be detected because of seasonal variability and background noise. 

Conclusions 

 Preliminary results of a spatially extensive water quality monitoring program 

in the FKNMS are reported. Quarterly sampling at 150 fixed stations began in 

March 1995 and continue at present and consists of 12 sampling events. 

Stratification of sites according to depth showed that temperature, dissolved 

oxygen, total organic carbon, and total organic nitrogen were significantly higher 

at the surface while salinity, nitrate, nitrite, ammonium, total phosphorus, and 

turbidity were greater in bottom waters. Stratification according to geographical 

region showed that the Upper Keys generally had lower nutrient concentrations 

than the Middle or Lower Keys. In the Lower Keys inorganic nitrogen and total 

phosphorus was elevated in the Backcountry area. The offshore 

Marquesas/Quicksands area exhibited the highest phytoplankton biomass 
 15 

(chlorophyll a) for any segment of the FKNMS. Declining inshore to offshore 

trends were observed for nitrate, ammonia, silicate, total organic carbon, total 

organic nitrogen, and turbidity for all oceanside transects. Total phosphorus 

concentrations in the Lower Keys transects decreased with distance offshore but 

increased along transects in the Upper Keys, mostly because of low 

concentrations alongshore. Stations stratified as being off land or channel/pass 

showed that those stations situated along channels/passes through the Keys had 

higher nutrient concentrations, phytoplankton biomass, and turbidity than those 

stations off land. The differences were statistically significant but the absolute 

differences were very small and not likely to be biologically important. The water 

quality of the FKNMS is put in perspective with data from 150 stations sampled in 

SW Florida Shelf, Florida Bay, Whitewater Bay, Ten Thousand Islands, and 

Biscayne Bay. It becomes clear from this analysis that the ambient water quality 

in the Lower Keys and Marquesas is most strongly influenced by water quality of 

the SW Florida Shelf, the Middle Keys by SW Florida Shelf and Florida Bay 

transport, the Backcountry by internal nutrient sources, and the Upper Keys from 

Florida Current intrusion. 
 16 

References 

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Technical supporting document. South Florida Water Management District. 

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quality in Florida Bay and Whitewater Bay by multivariate analysis: Zones of similar 

influence (ZSI). Estuaries 20: 743-758. 

BOYER, J. N., J. W. FOURQUREAN, AND R. D. JONES. 1999. Seasonal and long term trends in the 

water quality of Florida Bay (1989 - 1997). Estuaries 22: 417-430. 

BOYER, J. N., AND R. D. JONES. 1998. Influence of coastal morphology and watershed 

characteristics on the water quality of mangrove estuaries in the Ten Thousand Islands - 

Whitewater Bay complex. Proceedings of the 1998 Florida Bay Science Conference. 

University of Florida Sea Grant. 

BOYER, J. N., AND R. D. JONES. 1999. Effects of freshwater inputs and loading of phosphorus 

and nitrogen on the water quality of Eastern Florida Bay, p. 545-561. In K. R. Reddy, G. A. 

O’Connor, and C. L. Schelske [eds.] Phosphorus biogeochemistry in sub-tropical ecosystems. 

CRC/Lewis Publishers, Boca Raton, Florida. 

BRAND, L. 1998. The role of groundwater in the Florida Bay ecosystem. Proceedings of the 

1998 Florida Bay Science Conference. University of Florida Sea Grant. 

CAPONE, D. G., AND B. F. TAYLOR. 1980. Microbial nitrogen cycling in a seagrass community, 

p. 153-161. In V. S. Kennedy [ed.], Estuarine perspectives. Academic. 

DEPARTMENT OF COMMERCE. 1995. Florida Keys National Marine Sanctuary draft management 

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Sanctuary Programs Division. 245 p. 

ENVIRONMENTAL PROTECTION AGENCY. 1995. Water quality protection program for the Florida 

Keys National Marine Sanctuary: Phase III report. Final report submitted to the 

Environmental Protection Agency under Work Assignment 1, Contract No. 68-C2-0134. 

Battelle Ocean Sciences, Duxbury, MA and Continental Shelf Associates, Inc., Jupiter FL. 

FOURQUREAN, J. W., R. D. JONES, AND J. C. ZIEMAN. 1993. Processes influencing water column 

nutrient characteristics and phosphorus limitation of phytoplankton biomass in Florida Bay, 

FL, USA: inferences from spatial distributions. Estuar., Coast. Shelf Sci. 36: 295-314. 

FRANKOVICH, T. A., AND R. D. JONES. 1998. A rapid, precise, and sensitive method for the 

determination of total nitrogen in natural waters. Mar. Chem. 60: 227-234. 

FROELICH, P. N., JR., D. K. ATWOOD, AND G. S. GIESE. 1978. Influence of Amazon River 

discharge on surface salinity and dissolved silicate concentrations in the Caribbean Sea. 

Deep Sea Res. 25: 735-744. 

GARCIA, H. E., AND L. I. GORDON. 1992. Oxygen solubility in seawater: Better fitting equations. 

Limnol. Oceanogr. 37: 1307-1312. 

JONES, R. D. 1996. Phosphorus cycling, p. 343-348. In G. J. Hurst, G. A. Knudsen, M. J. 

McInerney, L. D. Stetzenbach and M. V. Walter [eds.], Manual of environmental 

microbiology. ASM Press. 

KIRK, J. T. O. 1994. Light and photosynthesis in aquatic systems, 2nd Ed. Cambridge. 

KLEIN, C. J., AND S. P. ORLANDO JR. 1994. A spatial framework for water-quality management 

in the Florida Keys National Marine Sanctuary. Bull. Mar. Sci. 54: 1036-1044. 

LAPOINTE, B. E., AND M. W. CLARK. 1992. Nutrient inputs from the watershed and coastal 

eutrophication in the Florida Keys. Estuaries 15: 465-476. 
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LAPOINTE, B. E., AND W. R. MATZIE. 1996. Effects of stormwater nutrient discharges on 

eutrophication processes in nearshore waters of the Florida Keys. Estuaries 19: 422-435. 

LEE, T. N., M. E. CLARKE, E. WILLIAMS, A. F. SZMANT, AND T. BERGER. 1994. Evolution of the 

Tortugas gyre and its influence on recruitment in the Florida Keys. Bull. Mar. Sci. 54: 621-

646. 

LEICHTER, J. J., S. R. WING, S. L. MILLER, AND M. W. DENNY. 1996. Pulsed delivery of 

subthermocline water to Conch Reef (Florida Keys) by internal tidal bores. Limnol. 

Oceanogr. 41: 1490-1501. 

MEEDER, J. F., J. ALVORD, M. BYRNS, M. S. ROSS, AND A. RENSHAW. 1997. Distribution of 

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NELSON, D. M., AND Q. DORTCH. 1996. Silicic acid depletion and silicon limitation in the 

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 18 

List of Tables 

Table 1. Summary statistics for each water quality variable in the FKNMS. Data are 

summarized as median (Median), minimum value (Min.), maximum value (Max.), and number 

of samples (n). 

Table 2. Physical and chemical differences between surface and bottom waters on 25 April 1998 

stratification event at 2 sites in the SW Tortugas (Segment 1) of the FKNMS. 
 19 

Table 1. 

 

 Median Min. Max. n 

NO3

-

 0.08 0.00 1.61 862 

NO2

-

 0.04 0.00 0.22 1180 

NH4

+

 0.27 0.01 2.44 1191 

TON 9.65 3.64 42.67 1180 

TP 0.17 0.01 0.66 1183 

SRP 0.01 0.00 0.12 915 

APA 0.04 0.01 0.84 1029 

Chl a 0.25 0.01 6.81 1188 

TOC 198.70 86.98 1054.79 1186 

Si(OH)4 0.59 0.00 37.36 902 

Turbidity 0.46 0.01 12.97 1083 

Salinity 36.20 31.80 38.40 1140 

Temperat

ure 26.45 17.50 39.60 1146 

DO 6.20 4.60 10.40 1123 

DOsat 92.50 68.28 150.03 1123 

Kd 0.16 0.01 1.12 1138 

TN:TP 62.10 15.89 1356.21 1181 

DIN:SRP 43.83 1.40 935.33 906 

%Io 17.21 0.00 97.03 1138 
 20 

Table 2. 

 

 Station #345 Station #350 

 Surface Bottom Surface Bottom 

Salinity 36.00 36.00 36.10 36.00 

Temperature 24.00 19.70 23.60 20.20 

NO3

-

 0.05 3.66 0.00 3.23 

NO2

-

 0.01 0.81 0.04 0.35 

NH4

+

 0.94 1.14 0.32 0.57 

TP 0.23 0.39 0.19 0.40 

SRP 0.02 0.22 0.01 0.20 

Si(OH)4 0.09 2.07 0.29 2.26 

TOC 170.10 155.48 171.42 168.35 

TON 4.86 2.25 5.45 4.01 

Chl a 0.94 1.62 1.10 1.82 

Turbidity 0.17 0.50 0.43 1.11 

DOsat 94.28 80.91 93.90 78.74 
 21 

List of Figures 

Fig. 1. The SERC Water Quality Monitoring Network showing the FKNMS boundary, segments, 

and distribution of sampling stations within the FKNMS, Florida Bay, Biscayne Bay, Whitewater 

Bay, Ten Thousand Islands, and Southwest Florida Shelf. 

Fig. 2. Box-and-whisker plots of NO3

-

, NH4

+

, TP, SRP, Si(OH)4, and Chl a stratified by FKNMS 

segment: 1 = Tortugas, 2 = Marquesas, 4 = Backcountry, 5 = Lower Keys, 6 = Sluiceway, 7 = 

Middle Keys, and 9 = Upper Keys. 

Fig. 3. Box-and-whisker plots of TOC, TON, APA, DOsat, salinity, and turbidity by FKNMS 

segment. 

Fig. 4. Box-and-whisker plots of temperature, Kd, TN:TP, and DIN:SRP by FKNMS segment. 

Fig. 5. Box-and-whisker plots of NO3

-

, NH4

+

, TP, Si(OH)4 by FKNMS segment and location on 

transect from land. In the Tortugas segment AS = alongshore, CH = channel, and OS = offshore. 

Fig. 6. Box-and-whisker plots of Chl a, TOC, turbidity, and salinity by FKNMS segment and 

location on transect from land. 

Fig. 7. Box-and-whisker plots of NO3

-

, NH4

+

, TP, Si(OH)4, Chl a , TOC, salinity, and turbidity 

for ocean-side Keys transects stratified as being located along Biscayne Bay National Park 

(BISC), against land in Key Largo, Middle and Lower Keys (LAND), or in line with major 

passes in the Keys (PASS). 

Fig. 8. Contour map of median salinity generated from fixed stations (+) in South Florida coastal 

waters. 

Fig. 9. Contour map of median delta sigma-t (∆σt in kg m-3) generated from fixed stations (+) in 

South Florida coastal waters reported as the median for 12 sampling events. ∆σt is the difference 

in density between surface and bottom waters where positive values mean bottom is more dense 

than surface. 

Fig. 10. Contour map of median Si(OH)4 (μM) generated from fixed stations (+) in South 

Florida coastal waters. 

Fig. 11. Contour map of median NO3

-

 (μM) generated from fixed stations (+) in South Florida 

coastal waters. 

Fig. 12. Contour map of median TP (μM) generated from fixed stations (+) in South Florida 

coastal waters. 

Fig. 13. Contour map of median SRP (μM) generated from fixed stations (+) in South Florida 

coastal waters. 
 22 

Fig. 14. Contour map of median TOC (μM) generated from fixed stations (+) in South Florida 

coastal waters. 

Fig. 15. Contour map of median Chl a (μg l-1) generated from fixed stations (+) in South Florida 

coastal waters. 

Fig. 16. Contour map of median turbidity (NTU) generated from fixed stations (+) in South 

Florida coastal waters. 

Fig. 17. Contour map of median DIN:SRP ratio generated from fixed stations (+) in South 

Florida coastal waters. 
 23 

Figure 1. 

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5 -80.0

24.5

25.0

25.5

26.0

Gulf of Mexico

Atlantic Ocean

Miami

1

4

2

5

9

7 Tortugas 6 Marquesas

Backcountry Sluiceway

Lower Keys

Middle Keys

Upper keys
 24 

Figure 2. 

0.0

0.2

0.4

0.6

0.8

1.0

1.2

μM

1 2 4 5 6 7 9

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

μM

1 2 4 5 6 7 9

0.0

0.1

0.2

0.3

0.4

μM

1 2 4 5 6 7 9

0.00

0.02

0.04

0.06

0.08

0.10

μM

1 2 4 5 6 7 9

0.0

5.0

10.0

15.0

20.0

μM

1 2 4 5 6 7 9

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

μg/l

1 2 4 5 6 7 9

NO3

TP

NH4

SRP

Si(OH)4 Chl a

Segment Segment
 25 

Figure 3. 

100

150

200

250

300

350

400

μM

1 2 4 5 6 7 9

4

6

8

10

12

14

16

18

20

22

μM

1 2 4 5 6 7 9

TOC TON

0.00

0.05

0.10

0.15

0.20

0.25

μM/hr

1 2 4 5 6 7 9

70

80

90

100

110

120

%

1 2 4 5 6 7 9

32

33

34

35

36

37

38

psu

1 2 4 5 6 7 9

0.0

1.0

2.0

3.0

4.0

NTU

1 2 4 5 6 7 9

Salinity

Segment Segment

Turbidity

APA DOsat
 26 

Figure 4. 

20

22

24

26

28

30

32

34

oC

1 2 4 5 6 7 9

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

1/m

1 2 4 5 6 7 9

Temperature Kd

20

40

60

80

100

120

140

1 2 4 5 6 7 9

0

50

100

150

200

250

300

1 2 4 5 6 7 9

TN:TP DIN:SRP

Segment Segment
 27 

Figure 5. 

0.0

0.2

0.4

0.6

0.8

1.0

1.2

μM

5 -A lo n g S h o re

5 -Cha n ne l

5 -Ree f

7 -A lo n g S h o re

7 -Cha n ne l

7 -Ree f

9 -A lo n g S h o re

9 -Cha n ne l

9 -Ree f

Ba c k c ou n try

Ma rqu e sa s

S lu ic e w a y

To rtug a s-A STo rtug a s-C hTo rtug a s-O S

NO3

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

μM

5 -A lo n g S h o re 5 -Cha n ne l 5 -Ree f 7 -A lo n g S h o re 7 -Cha n ne l 7 -Ree f 9 -A lo n g S h o re 9 -Cha n ne l 9 -Ree f Ba c k c ou n try Ma rqu e sa s S lu ic e w a y To rtug a s-A S To rtug a s-C h To rtug a s-O S

0.0

0.1

0.2

0.3

0.4

μM

5 -A lo n g S h o re

5 -Cha n ne l

5 -Ree f

7 -A lo n g S h o re

7 -Cha n ne l

7 -Ree f

9 -A lo n g S h o re

9 -Cha n ne l

9 -Ree f

Ba c k c ou n try

Ma rqu e sa s

S lu ic e w a y

To rtug a s-A STo rtug a s-C hTo rtug a s-O S

0.0

5.0

10.0

15.0

20.0

μM

5-AlongShore

5-Channel

5-Reef

7-AlongShore

7-Channel

7-Reef

9-AlongShore

9-Channel

9-Reef

Backcountry

Marquesas

Sluiceway

Tortugas-AS

Tortugas-Ch

Tortugas-OS

NH4

TP

Si(OH)4
 28 

Figure 6. 

0.0

0.2

0.4

0.6

0.8

1.0

1.2

μM

5 -A lo n g S h o re 5 -Ch a n n e l 5 -Re e f 7 -A lo n g S h o re 7 -Ch a n n e l 7 -Re e f 9 -A lo n g S h o re 9 -Ch a n n e l 9 -Re e f B ac k co u ntry Marq u es a s S lu ic e w a y T ortu g as -A S T ortu g as -C h T ortu g as -O S

Chl a

100

150

200

250

300

350

400

450

μM

5 -A lo n g S h o re

5 -Ch a n n e l

5 -Re e f

7 -A lo n g S h o re

7 -Ch a n n e l

7 -Re e f

9 -A lo n g S h o re

9 -Ch a n n e l

9 -Re e f

B ac k co u ntry

Marq u es a s

S lu ic e w a y

T ortu g as -A ST ortu g as -C hT ortu g as -O S

0.0

1.0

2.0

3.0

4.0

NTU

5 -A lo n g S h o re 5 -Ch a n n e l 5 -Re e f 7 -A lo n g S h o re 7 -Ch a n n e l 7 -Re e f 9 -A lo n g S h o re 9 -Ch a n n e l 9 -Re e f B ac k co u ntry Marq u es a s S lu ic e w a y T ortu g as -A S T ortu g as -C h T ortu g as -O S

32

33

34

35

36

37

38

psu

5-AlongShore

5-Channel

5-Reef

7-AlongShore

7-Channel

7-Reef

9-AlongShore

9-Channel

9-Reef

Backcountry

Marquesas

Sluiceway

Tortugas-AS

Tortugas-Ch

Tortugas-OS

TOC

Turbidity

Salinity
 29 

Figure 7. 

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

μM

BISC LAND PASS

0.0

0.2

0.4

0.6

0.8

1.0

1.2

μM

BISC LAND PASS

0.00

0.05

0.10

0.15

0.20

0.25

0.30

μM

BISC LAND PASS

0.0

1.0

2.0

3.0

4.0

5.0

6.0

7.0

8.0

9.0

μM

BISC LAND PASS

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

μg/l

BISC LAND PASS

100

150

200

250

300

350

μM

BISC LAND PASS

34

35

36

37

38

psu

BISC LAND PASS

0.0

0.5

1.0

1.5

2.0

NTU

BISC LAND PASS

NO3

TP

NH4

Si(OH)4

TOC

Salinity Turbidity

Chl a
 30 

Figure 8. 

Figure 9. 

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

-0.4

-0.2

0.0

0.2

0.4

0.6

0.8

1.0

delta Sigma-t

Median 1995-98

kg/m3

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

27

28

29

30

31

32

33

34

35

36

37

Salinity 38

Median 1995-98

psu
 31 

Figure 10. 

Figure 11. 

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

0

1

2

3

4

5

6

7

8

9

Silicate 10

Median 1995-98

uM

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1.0 Nitrate

Median 1995-98

uM
 32 

Figure 12. 

Figure 13. 

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

0.0

0.1

0.2

0.3

0.4

0.5 Total Phosphorus

Median 1995-98

uM

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

0.00

0.01

0.02

0.03

Soluble Reactive P

Median 1995-98

uM
 33 

Figure 14. 

Figure 15. 

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

100

200

300

400

500

600 Total Organic Carbon

Median 1995-98

uM

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

0.0

0.5

1.0

1.5

2.0

Chlorophyll a 2.5

Median 1995-98

ug/l
 34 

Figure 16. 

Figure 17. 

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

0

1

2

3

4

Turbidity 5

Median 1995-98

NTU

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

0

16

32

48

64

80

96

112

128

144

DIN:SRP Ratio 160

Median 1995-98