MISSISSIPPI RIVER AND TRIBUTARIES SYSTEM

2011 POST-FLOOD REPORT

APPENDIX F

ENVIRONMENTAL AND CULTURAL RESOURCES
Mississippi River and Tributaries System

2011 Post Flood Report

Appendix F

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F-IV-1

SECTION IV

Water-Quality and Phytoplankton Communities in Lake Pontchartrain before, during, and after the 

Bonnet Carré Spillway openings in 2008 and 2011, Louisiana. by Scott V. Mize, Dennis, K. 

Demcheck, and Brett W. Rivers

ABSTRACT

The periodic release of Mississippi River water into Lake Pontchartrain during exceptionally high 

flood years has the potential to affect the chemistry and ecology of the lake. The U.S. Geological 

Survey in cooperation with the U.S. Army Corps of Engineers monitored the chemical and ecological 

response of the 2008 and 2011 Mississippi river freshwater diversions into the normally brackish 

oligotrophic lake. Constituents monitored included major ions, nutrients, chlorophyll, phytoplankton, 

selected algal toxins, and triazine herbicides. Both events were similar in that the initial water-quality 

response was characterized by shifts in inorganic constituents such as chloride and inorganic nitrate. 

Emphasis shifted to biological effects as the lake system responded to the influx of freshwater and 

nutrients. The phytoplankton community in 2008 showed an extended response of bloom species 

within the lake to the influx of river water that was evident even after the water-chemistry indicated 

that the lake had returned to pre-diversion conditions. In contrast, in 2011 the community response of 

bloom species occurred much farther eastward in Mississippi Sound and in the lake outlet following 

Tropical Storm Lee.

The Bonnet Carré spillway delivered a maximum of about 169,000 cubic feet per second (cfs) from 

April 11-May 8, 2008 and a maximum of 314,000 cfs from May 9- June 20, 2010, nearly 3 times more 

volume than the amount discharged in 2008. Total suspended sediment concentration and the 

percentage of fines (silt and clay) in release water was higher in 2008 than in 2011. Estimated nutrient 

and sediment loads were determined from measured discharge and water-quality sample results 

collected from the spillway from 2008 and 2011. Nutrient and sediment load estimates for 2011, 

where 2 – 4 times larger than for 2008.

Spatial and temporal water-quality differences in spillway and lake samples from 2008 and 2011 were 

examined using Principal Components Analysis (PCA). Bonnet Carré Spillway inputs from the river 

into the lake differed temporally and were related to annual differences in the river water quality. 

Time-series trajectories were overlain on the PCA biplots to examine changes in lake water-quality 

characteristics between the 2008 and 2010 sampling periods (1-4). Lake samples at all locations 

(north, south, and outlets) in 2008 and 2011 were most similar during periods 1, time prior to arrival of 

river water at the Causeway and period 4, after river water had departed the lake. Water quality 

changes related to the river inputs were most evident in period 2, once river had reached the 

Causeway, and period 3, after river water departed the Causeway but before the diverted water had 

departed from the lake. The larger differences among 2008 and 2011 lake samples occurred during 

period 3. Period 3 samples in 2008 were high in calcium, chloride, magnesium, and sulfate, and 

chlorophyll a, and organic nitrogen and carbon. In 2011, samples in period 3 were more similar to 

river water and were high in nitrate, ammonia, atrazine, silica, phosphorous, and orthophosphate.

Time-series trajectories in period 4 indicated a gradual return to lake conditions prior to river water 

influence.
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Appendix F

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F-IV-2

Phytoplankton communities were used as indicators of water quality. Changes in phytoplankton 

composition corresponded to changing water-quality conditions in periods 1 through 4 in 2008 and 

2011. Phytoplankton community similarities were illustrated with non-metric multi-dimensional 

scaling two-dimensional ordinations. Both cell densities and biovolume measures of phytoplankton 

communities indicate community differences among sampling periods. The initial lake phytoplankton 

community response in 2008 to nutrient increases was related to accumulations of diatoms and green 

algae. During periods of low nutrient concentrations, bloom accumulations (> 90% biomass) of bluegreens occurred by July and August. Water-quality data indicated a gradual reversion to pre-diversion 

lake conditions by June to July, but shifts in the phytoplankton composition were still evident through 

September 2008. During 2011 phytoplankton communities in the lake were mostly composed of 

diatoms and cryptophytes. By July and August 2011, river water still influenced lake water quality and 

phytoplankton communities showed little variation in composition at mid-lake locations, yet 

Mississippi Sound phytoplankton samples were dominated (about 80% biomass) with bloom levels of 

blue-greens. By September 2011, post Tropical Storm Lee, the phytoplankton composition of the 

outlet and the Mississippi sound locations were composed mainly of saltwater species of 

dinoflagellates, green algae, and crytophytes. Although the lake exhibited a visual response to the 

freshwater influx, with dissolved oxygen exceeding 120% saturation, an obvious or prolonged algal 

bloom was not observed. A possible reason is that the massive and sustained diversion flow produced 

bloom conditions, but in Mississippi Sound rather than in Lake Pontchartrain in 2011. 

INTRODUCTION

The Bonnet Carré Spillway (Fig. 1), located 28 miles northwest of New Orleans, was constructed in the 

early 1930’s as part of an integrated flood-control system for the lower Mississippi River system. The 

spillway control structure consists of 350 individual bays or openings that can be opened to divert water 

from the Mississippi River to Lake Pontchartrain to relieve pressure on levees downstream. Heavy rains 

in the Mississippi and Ohio River valleys in early spring 2008 and in 2011 resulted in increased pressure 

on levees along the lower Mississippi River in Louisiana, threatening the City of New Orleans. In 

response, the U.S. Army Corps of Engineers opened the Spillway in April 2008 for the first time in 11 

years (U.S. Army Corps of Engineers, 2009) and again three years later in May 2011. In 2008, up to 160 

of the 350 bays were opened and in 2011 up to 330 of the 350 bays were opened and Mississippi River 

water flood waters were diverted into the 629-square mile Lake Pontchartrain. Lake Pontchartrain which 

is hydraulically connected to the Gulf of Mexico is more accurately characterized as an estuarine 

embayment. Peak flows through the spillway were about 169,000 cubic feet per second on April 22, 

2008 and 316,000 cubic feet per second from May 15- 20, 2011. 

Carefully managed freshwater diversions can provide positive water-quality effects in addition to 

flood control, but also for lake resources such as fisheries, sea grass production, and wetland 

restoration. An understanding of nitrogen, particularly nitrate, concentrations in the Lower Mississippi 

River and Lake Pontchartrain basins during hydrologic events such as high water is critical to 

understanding the flux of nutrients into Lake Pontchartrain and ultimately into the Gulf of Mexico. 

Nutrients from the Mississippi River basin could pose an environmental threat to the Gulf of Mexico, 

which is experiencing hypoxic areas and degradation of aquatic resources (Rabalais et al., 1996). After 

further analyses of the Pontchartain Estuary, ortch and Hird (2010) showed a need for further study of 

chlorophyll and algal data in Lake Pontchartrain and surrounding Mississippi Sound during spillway 

openings. In 2008 and again in 2011, the U.S. Geological Survey (USGS), in cooperation with the 

U.S. Army Corps of Engineers (USACE), began a study to assess the influence of river water from the 
Mississippi River and Tributaries System

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Appendix F

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F-IV-3

Mississippi River on water quality and phytoplankton (algae) communities in Lake Pontchartrain 

during and after the opening of the Bonnet Carré spillway.

NASA MODIS image, 4/29/08

The Rigolets

Crossover 7/Mile 9

Crossover 2

Chef Menteur Pass

Spillway at Hwy 61

Hwy 11 nr. Slidell

Figure 1. Sample locations at the Bonnet Carré Spillway and within Lake Pontchartrain

before, during, and after 2008 and 2011 spillway openings.

Purpose and Scope. This report characterizes surface-water quality and phytoplankton 

communities as indicators of surface-water quality for selected sites in Lake Pontchartrain before and 

after the Bonnet Carré Spillway opening in 2008 and 2011. A comparison of surface water quality 

conditions and algal communities is used to help refine the understanding of lake conditions both 

before and after flood events in which river water inputs have entered the lake. This report (1) 

compares 2008 and 2011 surface-water discharge, suspended sediment, and nutrient concentrations 

and loadings into the Lake Pontchartrain through the Bonnet Carré spillway; and (2) characterizes 

2008 and 2011 surface-water quality and phytoplankton community conditions spatially and 

temporally in the lake. 

Description of Study Area. The Lake Pontchartrain basin is a 629-square mile lake located in 

south-eastern Louisiana just north of New Orleans and is hydraulically connected to the Gulf of 

Mexico through two major passes (Rigolets and Chef Menteur Pass). The lake is more accurately 

characterized as an estuarine embayment in which a gradient of freshwater in the eastern portion of the 

lake changes to brackish water in the western portion of the lake near the lake outlets. Most natural 

freshwater inputs into Lake Pontchartrain include drainage from Lake Maurepas in the west and from 
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north shore drainages such as the Tangipahoa and Tchefuncte rivers as well as a few other bayous on 

the northeastern shore. During Bonnet Carré Spillway openings, Mississippi River water is diverted 

into Lake Pontchartrain via a 5-mile spillway located on the southwestern end of the lake.

Acknowledgments. The authors would like to thank the Greater New Orleans Expressway 

Commission for allowing access to crossovers on the Causeway Bridge. The authors would also thank 

Rodney Mach, and Eric Glisch, U.S. Army Corp of Engineers, New Orleans District, and Dr. Barb 

Kleiss, U.S. Army Corps of Engineers, Mississippi Valley Division for project development, and 

assistance and financial support with the study and report. Appreciation is extended to the following 

(USGS) employee Alexis Smith for assistance with sampling.

METHODS OF DATA COLLECTION AND ANALYSIS

Continuous and discrete sampling methods were used in 2008 and 2011. Continuous sampling using 

water quality monitor and a nitrate monitor located on the causeway in the southern part of the lake. A 

water-quality monitor and a nitrate monitor were suspended from the Lake Pontchartrain Causeway 

bridge about 10 feet below the water surface at crossover 7 – Mile 9 turnaround (about 15 miles east 

of the diversion and 3.5 miles from the south shore of the lake from April to July, 2008 and again from 

May to October, 2011 (Fig. 1). The lake depth at the site is about 16 feet. The monitors were equipped 

with internal loggers and recorded hourly measurements of nitrite + nitrate (presented as nitrate), 

water temperature, dissolved oxygen, specific conductance, salinity, and pH. Water-quality-monitor 

data were reviewed and, if where needed, corrected for instrument drift and biofouling following 

methods described in Wagner et al. ( 2006) prior to data analysis. Discrete surface-water samples were 

collected in the Bonnet Carrré Spillway and three other areas of the lake (north, south, and lake outlet) 

before, during, and after both 2008 and 2011 openings.

Sample Locations. Discrete water-quality samples were collected and analyzed for major 

inorganic ions, nutrients, chlorophyll a, atrazine, and phytoplankton. Samples were collected from one 

site within the Bonnet Carré Spillway about 2 miles downstream from the control structure, from three 

sites on the Lake Pontchartrain Causeway bridge, and from two sites, Rigolets at Hwy 90 near Slidell, 

LA (Rigolets), and Chef Menteur Pass at Chef Menteur, LA (Chef Menteur Pass) in 2008, and one site 

Highway 11 near Slidell, LA (Hwy 11) in 2011 on lake outflows into the Gulf of Mexico (Fig. 1). 

Samples at Lake Pontchartrain outflows were collected (to the extent possible) during outgoing tides 

to minimize the collection of estuarine waters from Lake Borgne and the Gulf of Mexico. Samples 

were collected weekly while the spillway was open and bimonthly after the spillway closure until 

October of each year, 2008 and 2011(Table 1).
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Table 1. Surface-Water Quality Phytoplankton Data-Collection Sites in the Lake Pontchartrain Basin in Southeastern Louisiana, 2008 and 2011

Sampling Period

U.S. Geological Survey 

Station Number U.S. Geological Survey Station Name

Descriptive Location

in Lake

April 2008

too Oct. 2008

May 2011

to Oct. 2011

300115090245000 Bonnet Carre Spillway at U S Hwy 61 near Norco, LA lake input x x

300412090084300 Lake Pontchartrain at Causeway Bridge nr Metairie, LA midlake (south) x x

300904090075200 Lake Pontchartrain at Causeway mile 9, near Metairie, LA midlake (south) x x

301528090064600 Lake Pontchartrain at Causeway near Mandeville, LA midlake (north) x x

301001089442600 Rigolets at Hwy 90 near Slidell, LA lake pass (outlet) x

300403089481300 Chef Menteur Pass at Chef Menteur, LA lake pass (outlet) x

301050089511600 Lake Pontchartrain at Hwy 11 Causeway nr Slidell, LA lake pass (outlet) x

300722089150100 Mississippi Sound near Grand Pass, LA Mississippi Sound1 x2

1 This sample is not located in Lake Pontchartrain but is located within the lake discharge into Mississippi Sound

2 This site was only sampled twice for phytoplankton in the summer.
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Data Analysis. Procedures used to collect and process water samples followed standard USGS 

guidelines (U.S. Geological Survey, 2001). Water samples were analyzed at the USGS National Water 

Quality Laboratory (NWQL) in Denver, Colo. using methods described by Fishman et al. (1989), 

Patton et al. (2000), Britton et al. (1987), Wershaw et al. (1987), and Sandstrom et al. (1992). 

Chlorophyll samples were collected using two different techniques. In 2008, chlorophyll samples were 

collected from the whole water column (equal depth integrated) and in 2011 sample were sampled just 

within the photic zone (approximately to top 1 meter of water). Chlorophyll samples were not adjusted 

for differences before data analysis, but 2008 sample are suspected to be underestimating the actual 

values. Phytoplankton samples were collected using National Water Quality Assessment Program 

protocols (Porter et al. 1993; Moulton et al. 2002). Phytoplankton samples were preserved with a 1 

percent Lugol’s solution and sent to the Academy of Natural Sciences in Philadelphia, Pa. for 

taxonomic analysis. Phytoplankton were identified and enumerated to practical taxonomic levels 

(normally species or genus level), following processing and analysis protocols according to Charles et 

al. (2002). 

Determinations of total discharge and loadings were based on measured discharge and chemical 

analysis results, yet in cases where daily discharge and or chemical analysis results were not available 

estimates were used in order to calculate loads. In 2008, daily discharge estimates were interpolated 

between measured discharge values. USACE calculated discharge values were used for 2011 missing 

daily discharge values. Chemical concentration results were not collected daily; therefore, chemical 

concentrations were interpolated between measured concentration values. Because discharge 

measurements within the Bonnet Carré Spillway can only be collected during diversion openings, too 

few discharge and concentration datasets exists to use load estimation methods based on long-term 

comprehensive or annual data. So, two methods commonly used for short-term events, such as storm 

events, were used to estimate solute loads at the Bonnet Carré Spillway at US highway 61, the average 

method and the period-weighted approach (Aulenbach, 2006). Each method uses daily discharge and 

concentration values to determine an instantaneous load for the day. Using the average method all 

daily discharge and sample concentrations collected during the spillway openings in 2008 and 2011 

were averaged respectively and multiplied to determine the loads for each opening by year. The 

period-weighted approach involved determining a daily discharge and daily sample concentration for 

each day of the opening for each year and calculating the instantaneous load for each day. The 

summation of all of the instantaneous loads for each opening was the final load estimate for each year.

Four critical sampling periods were selected for 2008 and 2011 water quality and phytoplankton 

samples based on continuous monitoring data, satellite imagery, and field observations to help 

describe physical, chemical, and biological changes in relation to the arrival and departure of river 

water into Lake Pontchartrain. These sampling periods were used to examine differences among 

sampling periods and years. 

Water quality and biological data sets were analyzed using a Plymouth Routines In Multivariate 

Ecological Research (PRIMER, version 6.0; Clark and Gorley, 2006). Water quality data were log 

transformed and normalized prior to entry in the principal components analysis (PCA). Trajectory 

plots were generated based on chronological order of sample collection by year and were overlain onto 

PCA biplots illustrating the chemical time- series patterns. Phytoplankton density data was fourth -root 

transformed to down weigh high abundance species prior to the generation of Bray-Curtis similarity 

resemblance matrices. Phytoplankton resemblance matrices were then represented as non-metric 

multidimensional (NMDS) ordination plots. Samples within a NMDS that plot that are closer to one 
Mississippi River and Tributaries System

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Appendix F

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F-IV-7

another have more similar composition; whereas, samples that plot further away from one another are 

less similar. The effectiveness of the NMDS plots in accurately representing the temporal relation at a 

given site was assessed with a two-dimensional stress value.

COMPARISON WATER QUALITY CHARACTERISTICS 2008 AND 2011

The amount and duration of spillway inputs varied between 2008 than 2011. Yearly spillway inputs 

from the river into the lake differed temporally and were related to annual differences in the river 

water quality and the quantity of diverted water. Generally, water quality samples from the lake 

showed little variation spatially, but larger differences were detected among temporal samples 

associated with the lake conditions prior to, during, and after the spillway openings. Comparisons 

between years and among time periods relieved some surface-water quality characteristics differed 

between the 2008 and 2010 samples from the Bonnet Carré Spillway and in lake samples. 

Bonnet Carré Spillway Inputs into Lake Pontchartrain. Discharge of Mississippi river water 

diverted through the Bonnet Carrré Spillway in 2008 and 2011 varied greatly in magnitude and 

duration (Fig. 2). Total volume of river water discharged in Lake Pontchartrain through the spillway in 

2008 was about 281 billion cubic feet or about 145% of the estimated lake volume (J. Lovelace, 

USGS, written communication 2008). The total volume discharged into the lake in 2011 was about 

780 billion cubic feet over 400% of the estimated lake volume and nearly 3 times more volume than 

the amount discharged in 2008. Peak discharge in 2008 (169,000 ft3

/s) was almost half that of 2011 

(314,000 ft3

/s). Also, the timing of the river diversion was different in 2008 compared to 2011. In 

2008, the river diversion open in April 2008 and lasted approximately 4 weeks (28 days), whereas the 

diversion in 2011 did not open until May 2011 and lasted approximately 6 weeks ( 44 days). 

Discharge and Suspended Sediment. Discharge and corresponding suspended sediment 

concentrations varied among 2008 and 2011 releases (Fig. 3). Total suspended sediment concentration 

and the percentage of fines (silt and clay) in release water was higher in 2008 than in 2011. The 

differences in rates of discharge flowing in the spillway in 2008 which was much lower than 2011 

may account for the differences in 2008 and 2011 suspended sediment samples. Samples in 2011 

contained lower percentages of fines which are more indicative of higher flow conditions that existed 

in 2011 and would be able to suspend more sand-sized particles. 
Mississippi River and Tributaries System

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Figure 2

Suspended sediment

• at Hwy 61 bridge: 1/3 of distance to the lake

86

88

90

92

94

96

98

100

0

20

40

60

80

100

120

140

160

180

200

0 10 20 30 40 50 60

PERCENTAGE FINES

TOTAL SUSPENDED SEDIMENT in milligrams per liter

Total Concentration and Percent Fines at Hwy 61

TSS Concentration (mg/L)

Percent fines (%)

2008 Release

2011 Release

Figure 3. Total Suspended Sediment and Percent Fines in 2008 and 2011 

from Highway 61 Bridge within the Bonnet Carré Spillway
Mississippi River and Tributaries System

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Appendix F

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F-IV-9

Nutrient Concentrations and Loadings. Estimated nutrient and sediment loads were 

determined using the average method and period-weighted approach (Aulenbach, 2006) from 

measured discharge and water-quality sample results collected at the Bonnet Carré Spillway from 

2008 and 2011. Total load estimates were determined for dissolved nitrite plus nitrate, total nitrogen, 

dissolved orthophosphate, total phosphorus, dissolved silica, and total suspended sediment (Table 2A). 

As expected, load estimates for 2011, where 2 – 4 times larger than for 2008. With the exception of 

dissolved orthophosphate and total suspended sediment, both the average and the period-weighted 

estimates produced loads with relative percent differences (RPD) of less than 10% among estimates 

(Table 2B). Higher RPDs up to 25 % were associated with dissolved orthophosphate and total 

suspended sediment. When comparing dissolved nitrite and nitrate and total nitrogen results in 2011 

from this study using the average and period-weighted approach estimates to the 2011 LOADEST 

estimations reported from Hypoxia in the Gulf of Mexico website estimates varied especially with 

total nitrogen loads which had RPDs over 130% (Table 2B). 

The large RPDs between load estimates in this study and LOADEST estimates may be related to 

computational differences in the load estimation calculations and/or that the loads were based on 

different measurements of the Mississippi River flow. Load estimates in this study were based on 

actual discharge and chemical results measured within the Bonnet Carré Spillway and not based on a 

percentage of flow diverted through the spillway. RPD of load estimates of the dissolved nitrite plus 

nitrate were only 50% or less, yet the total nitrogen estimates were much more variable (with RPDs up 

to133%) and may have been associated with the physical mechanics of spillway itself. Diverted 

Mississippi river water flowing into the pre-bay prior to entry into the spillway is capturing river water 

only from the upper portion of the water column which probably carries a lower suspended load than 

the middle and lower sections of the water column. Also, diverted river water once in the pre-bay has 

decreased in velocity and lost a portion of its suspended load prior to entering the spillway structure. 

This may account for the larger differences in load estimates in the total nitrogen fraction than the 

dissolved nitrogen fraction. 
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2011 Post Flood Report

Appendix F

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F-IV-10

Table 2A. Estimated nutrient and sediment loads in metric tons determined from measured discharge and water-quality sample results

collected at Bonnet Carre Spillway at U.S. Highway 61 near Norco, LA 2008 and 2011 [ d, days]

Estimated Loads in Metric Tons 

Estimation Method

Year

Sampled

Cumulative

Sampling Period

Dissolved Nitrite 

Plus Nitrate

Total

Nitrogen

Dissolved

Orthophosphate

Total

Phosphorus

Dissolved

Silica

Total

Suspended Sediment

Period-weighted approach1 2008 April (20d) 6,967 10,354 305 1,099 36,964 900,169

May (8d) 2,501 3,457 103 309 11,533 220,683

Total 9,468 13,810 408 1,408 48,497 1,120,852

2011 May (23d) 16,944 24,413 805 2,338 98,924 1,716,352

June (21d) 8,960 12,247 926 1,180 46,631 590,942

Total 25,904 36,659 1,731 3,518 145,555 2,307,294

Average method2 2008 Total 9,707 14,005 431 1,283 48,815 1,098,072

2011 Total 25,615 36,182 1,407 3,342 142,594 1,792,552

Reported LOADEST estimates3 2011 Total 15,500 180,000 -- -- -- --

Table 2B. Relative Percent Difference Among Total Load Estimates Determined For The Bonnet Carre Spillway, LA in 2008 and 2011

Relative Percent Difference of Total Loads

Estimation Method

Year

Sampled

Cumulative

Sampling Period

Dissolved Nitrite 

Plus Nitrate

Total

Nitrogen

Dissolved

Orthophosphate

Total

Phosphorus

Dissolved

Silica

Total

Suspended Sediment

Period-weighted approach1 2008 Total 2.49 1.40 5.54 9.3 0.65 2.05

Average method2 2011 Total 1.12 1.31 20.6 5.13 2.05 25.1

Period-weighted approach1 2011 Total 50.3 132 -- -- -- --

Reported LOADEST estimates3

Average method2 2011 Total 49.2 133 -- -- -- --

Reported LOADEST estimates3

1 Period-weighted approach as described by Aulenbach (2006); summation of instantaneous loads (daily discharge*daily parameter concentration*conversion factor) for cumulative sampling period 2 Average method as described by Aulenbach (2006); average load (average discharge*average parameter concentration*conversion factor) for cumulative sampling period 3 LOADEST estimations from Preliminary Spring 2011 discussions reported from Hypoxia in the Gulf of Mexico website<http://toxics.usgs.gov/hypoxia/mississippi/oct_jun/graphics.html >
Mississippi River and Tributaries System

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Spatial and Temporal Spillway and Lake Conditions in 2008 and 2011. Spatial and 

temporal water-quality differences in spillway and lake samples from 2008 and 2011 were examined 

using Principal Components Analysis (PCA). Bonnet Carré Spillway inputs from the river into the 

lake differed temporally and were related to annual differences in the river water quality. Time-series 

trajectories were overlain on the PCA biplots to examine changes in lake water-quality characteristics 

between the 2008 and 2010 sampling periods (1-4). 

Water Quality Characteristics. Generally, 2008 spillway samples had slightly higher 

concentrations of nitrate and ammonia than concentrations in 2011yet, chlorophyll a and atrazine was 

slightly higher in 2011 release water. Figure 4 shows results of PCA of water quality differences in 

monthly spillway samples. April 2008 and June 2011 samples varied from May samples in 2008 and 

2011. April samples from 2008 were high in ammonia and were associated with an ammonia peak in 

the Mississippi river in 2008. The 2008 ammonia peak in the Mississippi river ranged from 0 .77mg/L 

at St. Francisville to 0.137mg/L at Baton Rouge in March 2008 and were above the average peak level 

concentration of about 0.040 mg/L for recent (2009-2011) spring Mississippi samples. April 2008 

spillway samples concentrations only reached the average Mississippi river peak levels of around 

0.035mg/L and were nearly twice the concentrations of all other 2008 and 2011 spillway samples. 

May samples from 2008 and 2011 were most similar between years and slightly varied in nutrient 

concentrations and were either high in dissolved organic nitrogen or in phosphorous and silica. June 

2011 spillway samples contained higher concentrations of sulfate, calcium, magnesium, and 

orthophosphate than April 2008 samples or May 2008 and 2011 samples.

Overall lake conditions differed in 2008 and 2011. Generally, water quality in period 1, 2 and 4 were 

similar in 2008 and 2011, yet the largest differences occurred in sampling period 3 samples. 

Period 3 samples in 2008 were high in calcium, chloride, magnesium, and sulfate, and chlorophyll a, 

and organic nitrogen and carbon. In 2011, samples in period 3 were more similar to river water and 

were high in nitrate, ammonia, atrazine, silica, phosphorous, and orthophosphate. Silica concentrations 

in 2008 lake samples were significantly reduced in early June compared to silica concentrations at 

mid-lake locations in 2011 which remained high. Chlorophyll a concentrations in 2008 were much 

higher and tended to have a large broad peak whereas chlorophyll a concentrations in 2011 had a 

distinct bimodal distribution at mid-lake locations. Atrazine concentrations in lake samples also were 

different in 2008 being much lower than in 2011 samples at mid-lake and at the lake outlet. 
Mississippi River and Tributaries System

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Figure 4. Principal Components Analysis ordination biplots showing monthly differences in Bonnet Carre 

Spillway samples from 2008 and 2011. Sample coordinates in relation to chemical species indicate monthly 

differences in chemical concentrations; vectors indicate direction of higher concentration.

Figure 5 (south lake sites), 6 (north lake site), and 7 (lake outlet sites) show water chemistry results of 

lake samples from 2008 and 2011 on PCA biplots with time-series trajectories correlating to the 

sampling periods. The time-series arrows indicate the chronological sampling order and the show the 

temporal changes in water chemistry samples and the pathway in relation to the PCA vectors 

(chemical species). The evolution of chemical conditions is shown by following the arrow through the 

model. Each sample plots on the PCA biplot based on the chemical composition of the sample at the 

point in time the sample was collected. Sampling periods represent time periods of lake sampling 

related to the arrival and departure of river water into the lake and help to distinguish between pre and 

post diversion lake conditions.

Lake samples at all locations (north, south, and outlets) in 2008 and 2011 were most similar during 

periods 1, time prior to arrival of river water at the Causeway and period 4, after river water had 

departed the lake. Water quality changes related to the river inputs were most evident in period 2, once 

river had reached the Causeway, and period 3, after river water departed the Causeway but before the 

diverted water had departed from the lake. The larger differences among 2008 and 2011 lake samples 

occurred during period 3. Time-series trajectories in period 4 indicated a gradual return to lake 

conditions prior to river water influence.

In both 2008 and 2011, at Causeway Crossover 7 and Mile 9 (south lake) was the first lake location to 

receive diverted river water after the spillway had opened. Dramatic decreases in water temperature 

and specific conductance were evident in 2008 and 2011 and showed a rapid decrease as river water 

-4 -2 0 2 4

PC1

-4

-2

0

2

4

P

C

2

Month

April

May

June

BC040808

C042108

BC042908

BC050508

BC051308

BC052008

BC050911

BC051611

BC052511

BC060211

BC060811

BC061411

BC062211

Cl

SO4

Si

Ca

Mg

NO3

DON

TON

P

OP

NH4

ChlA

TOC

Azine
Mississippi River and Tributaries System

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F-IV-13

begin to dominate the water quality conditions along the south lake shoreline. Figure 5 shows the 

initial lake response and corresponding changes in water chemistry in period 2 were similar in 2008 

and 2011, yet during sampling period 3, 2008 and 2011 sample chemistries differed and 2008 samples 

were higher in calcium, chloride, magnesium, and sulfate, chlorophyll a, organic nitrogen and carbon 

whereas 2011 samples were higher in nitrate, ammonia, atrazine, silica, and orthophosphate.

Similar to the south lake, the north lake site at Causeway crossover 2 (Figure 6) showed similar 

patterns in water quality concentrations in periods 1,2 and 4 but period 3 differed. Nutrients including 

phosphorous, orthophosphate, nitrate, ammonia, and silica and atrazine concentrations were much 

higher in period 3 in 2011 than 2008. The presence of the high amount s of nutrients and atrazine 

indicate that river water dominated the north lake site in 2011 even during period 3 when river water 

influence in 2008 was minimal. The dominates of river water at the north lake site in 2011 may be due 

larger amount of river water discharged in 2011 and the river replaced much of the lake water until 

period 4 when tropical storm Lee helped flush the lake of river water. North lake 2008 samples in 

period 3 were dominated by higher concentrations of calcium, chloride, magnesium, and sulfate, 

chlorophyll a, and organic nitrogen and carbon.

Figure 7, shows the lake outlet time-series trajectories of water quality for one lake outlet site Rigolets 

at Highway 90 near Slidell in 2008 and the 2011 lake outlet site at Highway 11 Causeway near Slidell. 

Nearly identical to patterns observed at the mid-lake (north and south) sites, water quality in period 1 

and 4 showed that pre- and post- diversion conditions were similar although sample chemical 

compositions varied among outlet sites in 2008 and 2011. Outlet site chemical conditions in period 1 

and 4 in 2008 were different from 2011 partially because the location of the sites had changed between 

2008 and 2011. In 2008, the site was located in the lake pass where flow is constricted and velocities 

are faster as lake water exits into Lake Borgne and the site is heavily influenced by tidal fluctuations 

and higher salinity waters. While in 2011, the outlet site was relocated further inland to help decrease 

chemical variability associated with the tidal fluctuations and constricted flow. Sampling period 3, like 

at the mid-lake sites, outlet sites showed the greatest differences among 2008 and 2011 samples. 

Outlet samples in 2008, from period 3, had higher concentrations of calcium, chloride, magnesium, 

and sulfate, chlorophyll a, total organic carbon, and total organic nitrogen than 2011 outlet sample 

which were high in nitrate, ammonia, atrazine, silica, phosphorous, orthophosphate, and dissolved 

organic nitrogen. 
Mississippi River and Tributaries System

2011 Post Flood Report

Appendix F

Environmental and Cultural Resources

F-IV-14

A

B

Figure 5. Principal Components Analysis ordination biplots showing time series trajectories from 2008 (A) and 

2011 (B) sample coordinates in relation to chemical species from Causeway Crossover 7 and Mile 9, south lake, 

Lake Pontchartrain before, during, and after 2008 and 2011 Flood spillway openings. Numbers indicate sampling 

period (1, prior to arrival of river water at the Causeway; 2, once river water had reached the Causeway; 3, after 

river water departed the Causeway; 4, after river had departed the lake).

Lake Pontchartrain at Causeway Crossover 7 and Mile 9, LA (South lake), 2008

-4 -2 0 2 4

PC1

-4

-2

0

2

4

PC2

series08

1

2

3

4

Cl

SO4

Si

Ca

Mg

NO3

DON

TON

P

OP

NH4

ChlA

TOC

Azine

Lake Pontchartrain at Causeway Crossover 7 and Mile 9, LA (South lake), 2011

-4 -2 0 2 4

PC1

-4

-2

0

2

4

PC2

series11

1

2

3

4

Cl

SO4

Si

Ca

Mg

NO3

DON

TON

P

OP

NH4

ChlA

TOC

Azine
Mississippi River and Tributaries System

2011 Post Flood Report

Appendix F

Environmental and Cultural Resources

F-IV-15

A

B

Figure 6. Principal Components Analysis ordination biplots showing time series trajectories from 2008 (A) and 

2011 (B) sample coordinates in relation to chemical species from Causeway Crossover 2, north lake, Lake 

Pontchartrain before, during, and after 2008 and 2011 Flood spillway openings. Numbers indicate sampling 

period (1, prior to arrival of river water at the Causeway; 2, once river water had reached the Causeway; 3, after 

river water departed the Causeway; 4, after river had departed the lake).

Lake Pontchartrain at Causeway Crossover 2, LA (North Lake), 2008

-6 -4 -2 0 2 4 6

PC1

-4

-2

0

2

4

PC2

series08

1

2

3

4

Cl SO4

Si

Ca

Mg

NO3

DON

TON

P

OP

NH4

ChlA

TOC

Azine

Lake Pontchartrain at Causeway Crossover 2, LA (North Lake), 2011

-6 -4 -2 0 2 4 6

PC1

-4

-2

0

2

4

PC2

series11

1

2

3

4

Cl SO4

Si

Ca

Mg

NO3

DON

TON

P

OP

NH4

ChlA

TOC

Azine
Mississippi River and Tributaries System

2011 Post Flood Report

Appendix F

Environmental and Cultural Resources

F-IV-16

A

B

Figure 7. Principal Components Analysis ordination biplots showing time series trajectories from 2008 (A) and 

2011 (B) sample coordinates in relation to chemical species from Rigolets and Highway 11 Causeway, lake 

outlet, Lake Pontchartrain before, during, and after 2008 and 2011 Flood spillway openings. Numbers indicate 

sampling period (1, prior to arrival of river water at the Causeway; 2, once river water had reached the 

Causeway; 3, after river water departed the Causeway; 4, after river had departed the lake).

Rigolets at Highway 90 near Slidell, LA (Lake outlet), 2008

-4 -2 0 2 4 6

PC1

-4

-2

0

2

4

6

PC2

series08rig

1

2

3

4

Cl SO4

Si

CaMg

NO3

DON

TON

P

OP

NH4

ChlA

TOC

Azine

Highway 11 Causeway near Slidell, LA (Lake outlet), 2011

-4 -2 0 2 4 6

PC1

-4

-2

0

2

4

6

PC2

series11

1

2

3

4

Cl SO4

Si

CaMg

NO3

DON

TON

P

OP

NH4

ChlA

TOC

Azine
Mississippi River and Tributaries System

2011 Post Flood Report

Appendix F

Environmental and Cultural Resources

F-IV-17

Phytoplankton as Indicators of Water Quality. Phytoplankton communities were used as 

indicators of water quality. Changes in phytoplankton composition corresponded to changing waterquality conditions in periods 1 through 4 in 2008 and 2011. Phytoplankton community similarities 

were illustrated with non-metric multi-dimensional scaling (NMDS) two-dimensional ordinations. 

Both cell densities and biovolume measures of phytoplankton communities indicate community 

differences among sampling periods related to the arrival and departure of Mississippi river flood 

water into Lake Pontchartrain 2008 (Figure 9) and 2011 (Figure 10 in process).

The 2008 NMDS plot of phytoplankton community composition shows the spatially similarities 

among lake sites, yet compositions differed temporally corresponded with sampling periods in the lake 

(Figure 9). An NMDS ordination with a stress level of 0.11 indicates a good representation of 

community compositions among samples according to Clark & Warwick (2001). As expected, the 

composition of phytoplankton at the Spillway (river water) in 2008 during period 1 differed from all 

other period 1 lake samples. One outlier, the 2008 Chef Menteur Pass outlet site had a different 

community structure than other period 3 and 4 lake sites that grouped together in the NMDS. The 

grouping of the period 3 and 4 samples indicates that during these sampling periods the composition of 

phytoplankton were similar and were dominated by blue-green algae as shown in Figure 11.

The initial lake phytoplankton community response in 2008 to nutrient increases was related to 

accumulations of diatoms (Fig. 11). During periods of low nutrient concentrations, bloom 

accumulations (> 90% biomass) of blue-greens occurred by July and August. As blue-green algae cell 

densities and biovolumes increased in the summer so did the species richness of blue-green algae, 

particularly the harmful algae bloom taxa. Cell densities and biovolume of the phytoplankton lake 

indicator taxa Skeletonema costatum, Anabaena sp. and Cylindrospermopsis raciborskii were highest 

and dominated the diatom and blue-green algae communities during the period of most river water 

influence on the lake and immediately following the freshwater inflows. The dominance and recession 

of these indictor taxa reflect the dramatic changes that occurred in the phytoplankton community in 

response to an increase in nutrient-rich freshwater from the diversion into the lake and not normal 

seasonal phytoplankton compositional differences. Water-quality data indicated a gradual reversion to 

pre-diversion lake conditions by June to July, but shifts in the phytoplankton composition were still 

evident through September 2008.
Mississippi River and Tributaries System

2011 Post Flood Report

Appendix F

Environmental and Cultural Resources

F-IV-18

Figure 9 Phytoplankton community similarities illustrated with non-metric multi-dimensional scaling (MDS) 

two-dimensional ordinations. Both cell densities and biovolume measures of phytoplankton communities 

indicate community differences among time periods related to the arrival and departure of Mississippi River 

flood water into Lake Pontchartrain, 2008.

Cell density08 Transform: Fourth root

Resemblance: S17 Bray Curtis similarity

time

1

2

3

4

Spillw ay

NorthL

NorthL

NorthL

NorthL

SouthL

SouthL

Outlet

Outlet

Outlet

Outlet

SouthL

SouthL

Outlet

Outlet

2D Stress: 0.11

biovolume08

Transform: Fourth root

Resemblance: S17 Bray Curtis similarity

time

1

2

3

4

Spillway

NorthL

NorthL

NorthL

NorthL

SouthL

SouthL

Outlet

Outlet

Outlet

Outlet

SouthL

SouthL

Outlet

Outlet

2D Stress: 0.11
Mississippi River and Tributaries System

2011 Post Flood Report

Appendix F

Environmental and Cultural Resources

F-IV-19

Phytoplankton taxa composition,

Spillway & 4 lake sampling periods, Apr. 8- Oct. 3, 2008

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

River Period 1 Lake Period 1 Lake Period 2 Lake Period 3 Lake Period 4

Sampling Periods

Dominant Phytoplankton Taxa, median 

percent biovolume in cubic micrometers 

alga per milliliter of sample

Dinoflagellata

(dinoflagellates) 

Cyanobacteria

(blue-green algae) 

Cryptophyta

(cryptophytes) 

Chlorophyta

(green algae) 

Bacillariophyceae

(diatoms) 

Other algae

Period 1: 4/8-22 Period 2: 4/29-5/29 Period 3: 6/03-7/16 Period 4: 8/04-10/03

Figure 11. Composition of dominant phytoplankton taxa for the Bonnet Carre Spillway,

and four sampling periods at five sites in Lake Pontchartrain, April to October 2008.

During 2011 phytoplankton communities in the lake were mostly composed of diatoms and 

cryptophytes. By July and August 2011, river water still influenced lake water quality and 

phytoplankton communities showed little variation in composition at mid-lake locations, yet 

Mississippi Sound phytoplankton samples were dominated (about 80% biomass) with bloom levels of 

blue-greens. By September 2011, post Tropical Storm Lee, the phytoplankton composition of the 

outlet and the Mississippi sound locations were composed mainly of saltwater species of 

dinoflagellates, green algae, and crytophytes. Although the lake exhibited a visual response to the 

freshwater influx, with dissolved oxygen exceeding 120% saturation, an obvious or prolonged algal 

bloom was not observed. A possible reason is that the massive and sustained diversion flow produced 

bloom conditions, but in Mississippi Sound rather than in Lake Pontchartrain in 2011.

A combination of factors influenced the water quality and phytoplankton communities in 2008 and 

2011. The nature and characteristics of the spillway openings themselves were different in magnitude 

and duration in 2008 and 2011. In addition to the increase in freshwater from the spillway in 2011, the 

closure of the Inter Harbor Navigation Canal (IHNC) in New Orleans along the south shore of the lake 

prior to the 2011 spillway opening has helped to decrease the salinity in the lake especially in the 

vicinity of canal. All of these factors that have contributed to the reduction of salinity in the lake and 

push the freshwater-saltwater interface from within the lake in 2008 to outside of the lake into the 

Mississippi Sound in 2011. 
Mississippi River and Tributaries System

2011 Post Flood Report

Appendix F

Environmental and Cultural Resources

F-IV-20

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Mississippi River and Tributaries System

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Appendix F

Environmental and Cultural Resources

F-IV-21

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