Wayne Magley

FDEP Division of Environmental Assessment 

and Restoration
Geographical and 

Physical Description

Located on northern east coast of 

Florida

Lower St. Johns River extends 

from mouth of Ocklawaha River to 

Atlantic Ocean (about 101 miles)

Water surface area of 115 square 

miles

A sixth-order, darkwater river 

estuary, and, along its length, it 

exhibits characteristics associated 

with riverine, lake, and estuarine 

aquatic environments

Tidal influence ranging from 0.35 

to 5.49 ft depending upon location

 A low gradient (averages 0.1 

ft/mile) elongated riverine-estuary 

system

Average depth of less than 3 m
o Low-head, lacustrine, humid/subtropical blackwater river estuary of the 

southeastern U.S.

o Mean discharge 235 m3/sec

o Southern-most natal river for eastcoast anadromous fish

o Large tide range (1.5 m) propagated 

200 km upstream

o Tidal flow >> Net Discharge

o Tidemarsh habitat 

o Significance:

o Major SE U.S. port

o 2 large military bases

o Important commercial and 

recreational fisheries

o Significant cultural and aesthetic 

resource (American Heritage River)
Geographical 

and Physical 

Description

Four ecological zones, 

based on salinity

There is a shift in land 

use from wetland, open 

land and agriculture in the 

southern portion of the 

basin to a highly 

urbanized area 

(Jacksonville/Duval 

County) in the mesopolyhaline zone
Waterbody 

Identification 

Numbers for 

the Main Stem 

of the LSJR 
Fresh Tidal Water Quality Time Series 

Example
Fresh Tidal Water Quality Time Series 

Example
Oligohaline Zone Water Quality Time Series 

Example
Oligohaline Zone Water Quality Time Series 

Example
Meso-Polyhaline Zone Water Quality Time Series 

Example
Meso-Polyhaline Zone Water Quality Time Series 

Example
 Springs and Ground water: There are 18 springs within 

the LSJR Basin, 9 of the springs are considered 

magnitude 3 springs (discharge 1 – 10 cfs. Morris 

(1995) reported that the USGS estimated the net upward 

leakage from ground water into the river of 82 cfs for WY 

1990 (a relatively dry year) and about 127 cfs under 

more normal conditions.

 Wastewater: Within the LSJR Basin 112 facilities are 

authorized to discharge to surface waters under an 

NPDES permit. The nutrient TMDL and BMAP for the 

LSJR provided allocations for 36 facilities (32 domestic 

wastewater facilities and 4 industrial wastewater 

facilities) that discharged directly into the Lower St. 

Johns or below the head of tide to tributaries that 

discharged into the river.
 Atmospheric Deposition: Pollman and Roy 

(2003) estimated a total annual flux of wet and 

dry inorganic nitrogen of 4.67 to 6.82 kgN/ha, 

with an average value of 6.12 kgN/ha. The 

annual average wet deposition of total 

phosphorus over the 1994 – 1999 period was 

estimated to range between 4.5 and 12.4 

kgP/km2, with an average of 8.25 kgP/km2. 

 Nonpoint Source Discharges: Stormwater from 

urban and rural areas. Twelve major tributary 

watersheds have been identified as contributing 

flow to the Lower St. Johns River.
 Low Dissolved Oxygen: Periods of low DO 

observed in meso-polyhaline zone based on 

continuous monitoring since 1995. Typically during 

the July – September period.

 Chlorophyll a: Concentrations in fresh tidal zone 

exceed 20 ug/L, during blooms, values over 60 ug/L. 

 Nuisance or toxic algal blooms: Periodic 

occurrences of nuisance and toxic algae blooms 

during the summer. Seven known or potentially 

toxic or harmful algal species have been identified in 

the LSJR. 
Fish Kills: Periodic fish kills have been observed in 

both the fresh water and marine portions of the LSJR, 

especially during summer periods.

Reduced Clarity: Color levels are elevated and 

water clarity is reduced during periods of increased 

fresh water discharges from upstream and tributaries.
Nuisance and Harmful Algal Blooms in the St. Johns River Estuary:

Mechanisms of Development and Species of Concern

 Flow determines 

dinoflagellate or bluegreen 

dominance

 Most likely to exhibit HAB 

species, particularly 

Microcystis aeruginosa

Oligohaline Reach Marine Reach and 

Atlantic Inner Shelf

 Integrates shelf and 

oligohaline environments

 Occasional contain HAB 

species Karenia brevis (red 

tide) & Pseudo-nitzschia

Fresh Tidal Reach

 Highest density of SJRE, 

dominated by cyanobacteria

 Density positively correlated 

with residence time

 Significant water quality 

problems
 Verified list of Impairments for the Cycle 1 Assessment for the 

Lower St. Johns River Basin (adopted in May 2004) included 

28 waterbodies for nutrients. Sixteen listings for DO were 

associated with elevated algal biomass or linked to nutrients 

based on median TN and/or TP concentrations. There were 6 

predominantly marine WBIDs listed for nutrients. 

 Verified list of Impairments for the Cycle 2 Assessment 

(adopted in May 2009 and amended in January 2010) 

included 29 listings for nutrients. Eighteen listings for DO 

were associated with elevated algal biomass or linked to 

nutrients based on median TN and/or TP concentrations. 

There was 1 predominantly marine WBID listed for nutrients 

and none listed for DO
 In August 2008, FDEP re-adopted the nutrient 

TMDL for the Lower St. Johns River.

 Allowable annual loads for TN and TP were 

assigned to the fresh water portion (fresh tidal 

zone) based upon the pollutant load reduction 

goal (PLRG) developed by the SJRWMD.

 Allowable annual loads for TN were assigned 

to the marine portion (oligohaline and mesopolyhaline zones) based on the PLRG.
Lower St. Johns Water Quality 

Model Grid, Watersheds and 

Point Sources ( ) 

TMDL Tools: 

• Quasi-dynamic version of the classic 

spreadsheet land use loading model for 

NPS

- Being upgraded to assess ERP

urban development 

• Adaptation of CE-QUAL-ICM 

(Chesapeake Bay Eutrophication Model) 

to the LSJR

- Expanded through L. George

and 2005

• Specific monitoring and investigations 

related to chemistry, plankton, nutrient 

limitation, atmospheric deposition, and 

sediment flux. 

Linking Degree of Effects to the Biological Community: St. 

Johns R. Estuary Eutrophication Models
• Chlorophyll-a > 40 μg/L generally 

recognized as nuisance condition

• Corresponds to FL TSI = 70

• Established criteria (North Carolina, 

Lake Okeechobee)

• In LSJR:

– Community composition above 40 μg/L is 

> 80% cyanobacteria

– Chlorophyll-a > 40 μg/L for > 40 days 

associated declines in “good” 

zooplankton

– In nutrient enrichment assays, the 

incidence of high microcystin 

concentration increased when 

chlorophyll-a exceeded 40 μg/L 

LSJR Fresh Tidal Criteria

0

0.2

0.4

0.6

0.8

1

0 50 100 150 200

Cyanobact Biovol / Total Biovol

Chl-a ug/L

Cyano Dominance vs Chl (Apr-Oct) 

LG

Pal

Racy
LSJR Marine Reach 

Dissolved Oxygen

August 1999
LSJR Dissolved Oxygen SSAC

• Based on the EPA Ambient 

Aquatic Saltwater Criteria 

(Virginian Province; EPA822-R-00-012)

• Designed to protect 

against effects from longterm (days to weeks) low 

D.O. 

• Limits low D.O. exposure to 

no more that 5% loss of 

most sensitive species

MAX CHRONIC IMPAIRMENT

YEAR ACOSTA DAMES

1996 0.03 0.25*

1997 0.37 1.74

1998 0.73 0.56

1999 0.10 3.57

2000 0.26 0.20

2001 0.19 1.07
Lower St. Johns

Proposed Numeric Nutrient Criteria

The Department proposes to adopt the annual TMDL nutrient loads for the 

marine portion of the LSJR as load based numeric nutrient criteria that would 

apply to the marine portion of the LSJR (see Table).

 And adopt the annual TMDL TN and TP loads for the freshwater portion of 

the river as downstream protection values that will protect the LSJR estuary. 

The Chla target of 40 ug/L not to be exceeded more than 10% of the time is 

proposed as a numeric nutrient target applicable to the tidal freshwater portion 

of the LSJR as a long-term average. 

Freshwater 

WBIDs

Parameter TMDL

(kg/yr)

2213I to 2213N Total Nitrogen 8,571,563

2213I to 2213N Total Phosphorus 500,325

Marine WBIDs Parameter TMDL

(kg/yr)

2213A to 2213H Total Nitrogen 1,376,855
Waterbody 

Identification 

Numbers for 

the Main 

Stem of the 

LSJR 
Numeric Nutrient Criteria Considerations

Criteria include magnitude, frequency, and duration components. 

Expressed as loads, concentrations, or both?

The document presents some initial work on approaches to 

developing numeric concentrations. 

How should the criteria be assessed in the future?

Interested in public input!

Acknowledgements

 John Hendrickson and Dr. Peter Suscy at the SJRWMD were 

responsible for the main work that constitutes the scientific basis 

for the Total Maximum Daily Load.

Dr. Edward Phlips from the Department of Fisheries and Aquatic 

Sciences at the University of Florida for sharing his research on 

phytoplankton dynamics and work to support numeric nutrient 

criteria. 

Link: http://www.dep.state.fl.us/water/wqssp/nutrients/estuarine.htm