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Measuring Connectivity of 

Floodplain Waterbodies to 

the Lower Mississippi River

by Amanda J. M. Oliver, Catherine E. Murphy, Charles D. 

Little, Jr., and K. Jack Killgore

MRG&P Tech Note No. 1 • October 2016

Mississippi Valley Division Engineer Research and Development Center
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MRG&P Tech Note No. 1

INTRODUCTION: Prior to levee construction, Mississippi River floodwater spread across a 30-

to 124-mile-wide floodplain, exchanging nutrients, sediment, and organisms between the main 

channel and floodplain waterbodies. Levees now constrict the floodplain to an average 5-mile 

width and thus also reduce the number of waterbodies that the river can connect to (Biedenharn et 

al. 2000). Additionally, Lower Mississippi River (LMR) bendway cutoffs have increased the 

river’s slope and stream power (Biedenharn et al. 2000), potentially changing connectivity. 

Maintaining a gradient of connectivity—from waterbodies that are always connected to those that 

are rarely connected—is essential for ecosystem health (Ward and Tockner 2001). Rarely 

connected waterbodies support unique species assemblages (Tockner and Stanford 2002) and 

ecosystem diversity (Lubinski et al. 2008; Thomaz et al. 2007) while more frequently connected 

waterbodies can sequester and exchange nutrients from the main channel and provide areas for 

spawning, rearing, and refuge for riverine organisms (Baker et al. 1991; Stoffels et al. 2014). The 

U.S. Army Corps of Engineers has the ability to change connectivity by notching dikes, dredging 

to remove sand plugs and to maintain tie channels, and strategically placing revetment and dikes. 

To quantify connectivity and evaluate habitat restoration potential, a study was initiated 

encompassing the river and floodplain downstream of Helena, Arkansas, extending from 

approximately River Mile (RM) 620 to 642. This area was selected because of available longterm gage data, elevation data, accessibility, and the presence of numerous waterbodies that ideally

were discrete and arrayed along a gradient of connectivity. 

The study attempted to answer 

several questions, one of which was 

how the biological community and 

biogeochemical processes differ 

between waterbodies with different 

degrees of connection. Elevation 

data and gage data were used to 

locate connecting channels, to 

identify connection thresholds and 

locations, and to determine 

connection frequency. Ward et al. 

(1999) define connectivity as the 

transfer of water and material between the river’s main channel and the floodplain. A connection 

threshold is “the elevation river water must reach to enter” or, conversely, the elevation below 

which “water cannot gravity drain from” a discrete waterbody (Cobb et al. 1984) (Figure 1). This 

technical note documents a portion of the study: the data and methods to develop an elevation 

model and to determine connection thresholds and connection frequency. 

Figure 1. Illustration of the location of a connection threshold 

between two discrete waterbodies.
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METHODOLOGY: Bare-earth elevation data were gathered from aerial and bathymetric surveys 

and used to create a continuous computer model of the ground in the Island 63 project area. Within 

the model, the channels connecting floodplain waterbodies to the Mississippi River main channel 

were investigated to locate the highest elevation, or connection threshold, within the channel. The 

connection threshold was then compared to observed river gage water surface elevations to 

determine the frequency of connection between each floodplain waterbody and the river. 

Elevation Data. Light Detection and Ranging (LiDAR) and bathymetric elevation data were 

gathered to create a continuous bare-earth model of the project area, including river and lake beds

(Table 1). The most current and a second older, more complete set of aerial LiDAR data were 

compiled for the project area. The LiDAR technique determines ground elevation by transmitting 

a laser beam towards the earth, measuring the strength of the reflected beam, converting reflected 

strength to distance (range), and subtracting the distance from the known elevation of the receiver. 

The laser beam cannot penetrate turbid water, thus bathymetric data were acquired for submerged 

areas (Figure 2). 

Table 1. The source and native horizontal and vertical reference of elevation data used in this study.

Data Source Horizontal Vertical Vertical 

Accuracy

Horizontal 

Accuracy

2005 

LiDAR

St. Louis 

District 

(MVS)

WGS 84, UTM Z15N,

U.S. Survey ft*

NAVD88 (Geoid 03) , 

U.S. Survey ft

2009 

LiDAR

Earth 

Explorer

NAD83, State Plane 

MS W, U.S. Survey ft

NAVD88 (Geoid 03) , 

U.S. Survey ft <+0.5 sFT† <+1.65 sFT †

2013 

Bathymetry

Memphis 

District 

(MVM)

WGS 84, UTM Z15N,

U.S. Survey ft 

NAVD88 (Geoid 03) , 

U.S. Survey ft

2014 

Bathymetry MVM WGS 84, UTM Z15N,

U.S. Survey ft 

NAVD88 (Geoid 03) , 

U.S. Survey ft

+0.3 sFT ‡ +0.5 sFT ‡

2015 

Bathymetry

ERDCCHL§

NAD83, UTM Z15N, 

meters

NAVD88 (Geoid 12A||), 

meters * One U.S. survey foot (sFT) is equal to 0.30480061 while an international survey foot is equal to exactly 0.3048.

† Accuracy information represents equipment error after post processing (Aeroquest 2011).

‡ MVM provided accuracy information that represents equipment error after post-processing. 

§ U.S. Army Engineer Research and Development Center Coastal and Hydraulics Laboratory

|| As per the National Geodetic Survey (NGS) Interactive Computations page, elevation in the Island 63 area differs by an average of 0.36 ft between 

Geoid 03 and Geoid 12A (NGS 2015).
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Figure 2. (A) Extent of 2009 LiDAR and areas where 2005 LiDAR were added. White space 

represents submerged areas with no LiDAR data. (B) Elevation model with study 

sites labeled: MBP = Modoc Borrow Pits, I63 = Island 63 Secondary Channel, GrB = 

Graveyard Blue Hole, ORC = Old River Chute, McW = McWilliams Lake, JmS = Jim 

Samples Lake, GlH = Glory Hole Lake, I64 = Island 64 Secondary Channel, DsL = 

Desoto Lake, Mlw = Mellwood Lake, and SfD = Sunflower Dikes Secondary Channel.

One set of LiDAR data was downloaded from the U.S. Geological Survey (USGS) Earth Explorer 

as laser (LAS) files (USGS 2015). These data were originally collected from 19 February 2009 to 

2 August 2010 (Table 1). Data extended across the majority of the project area and were collected 

as points with a 1 m2 average spacing (Figure 2) (Aeroquest 2011). LAS file versions 1.1 onward

contain a classification scheme (0 = never classified, 1 = unassigned, 2 = bare earth, etc.). To 

investigate the classification scheme and check data quality, a LAS dataset was created in ArcGIS,

and the downloaded LAS files were loaded into it. Statistics were generated to determine point 

spacing, Z minimum, Z maximum, classifications, and total number of points (see ESRI 

[Environmental Systems Research Institute] 2008 for techniques and an in-depth discussion). 

Afterwards, the LAS files underwent two processing steps in RiSCAN Pro (RIEGL 2015). The 

first step generated a bare-earth dataset from the LAS files by removing all vegetation, building,

and water classifications. Next, to improve processing speeds, the Octree filter was used to 

decrease point density in flat areas based on user-designated thresholds for horizontal distance and 

elevation change. The end products were ArcGIS multipoint files. The second set of LiDAR data
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MRG&P Tech Note No. 1

was acquired in 2005 at a lower water surface elevation than the 2009 data. These data were 

provided as multipoint files by the St. Louis District, U.S. Army Corps of Engineers (USACE),

and were used to fill in areas of missing data within the project area (Figure 2).

For study waterbodies where there were no LiDAR data, bathymetric data were gathered. In 2013, 

bathymetric transect data were gathered in 1000 ft intervals by side-scan sonar. Each transect was

perpendicular to flow, and the survey encompassed the Mississippi River main channel and 

connected secondary channels. The Memphis District gathered multibeam bathymetry in 2014 for 

the Island 63 secondary channel, and ERDC-CHL gathered additional data on 7–8 April 2015 for 

the five small waterbodies southwest of Island 63. 

Bathymetric data were gathered in 2014 using a Reson SeaBat® 7101-ER multibeam echosounder 

and in 2015 by an Odom Echotrac® CV300 echosounder (Teledyne Thousand Oaks, CA) outfitted 

with a 240 kHz and 200 kHz transducer, respectively. The echosounder emits a sound pulse and 

records the time it takes for the sound pulse to bounce off the floor of the waterbody and be 

received by the echosounder’s microphone. By calibrating the equipment to the speed that sound 

travels through the location’s water, time can be converted into distance, which is subtracted from 

the water surface elevation to determine the bed elevation. Horizontal position for each bed 

elevation point (latitude and longitude) were received by a Trimble® R8 RTK GPS receiver 

(Trimble Navigation Limited, Sunnyvale, CA) from two Trimble® R8 base stations (survey-grade 

GPS units) centered on NGS control points (benchmarks). The base stations transmitted position 

correction information at random intervals to the receiver. This information along with gage 

readings was used to create water-level files that were edited and paired with echosounder readings 

by HYPACK® software (Xylem Brand, Middletown, CT) to yield a X, Y, Z file (ASCII). These 

files were then converted into ArcGIS multipoint files by using the ASCII 3D to Feature Class tool 

(ESRI 10.2, Redlands, CA).

Elevation Modeling. To display the elevation data and locate connection thresholds, a bareearth model of the project area was created in the form of an ArcGIS terrain model (Figure 2). To 

create the model, all bathymetry and LiDAR data were converted into a common horizontal 

projection (NAD1983 UTM Zone15N). Vertical projection and Geoid were also investigated to 

understand the vertical variation introduced and to control for this where possible. Data were then

combined within an ArcGIS feature dataset, and the terrain model was created from this dataset. 

Terrain parameters were 5 ft point spacing, window size pyramid type, point selection method of 

Z minimum with no secondary thinning, and five pyramid levels. A terrain model is the newer 

version of an ArcGIS Triangulated Irregular Network (TIN) model. Pyramids (lower resolution

versions) allow terrain models to draw and process faster than TIN models, but terrains still contain 

and use the full data for calculations. As with TINs, terrain models generate a surface by creating 

a network of triangles following the Delaunay triangulation method. A terrain model was chosen 
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over a raster (digital elevation model, DEM) because the triangulation method allows unique 

elevation values across the entire surface. For a full discussion of terrain design, see ESRI (2016). 

Connection Thresholds. Once 

the model was created, it was visually 

studied to identify and digitize all 

channels that connect to the study

sites. Any high areas within these 

channels were identified as potential 

connection thresholds (Figure 3). 

Connection-threshold identification 

was aided by creating profile graphs 

of the digitized channels (3D Analyst, 

ESRI 10.2, 2013). Thresholds with 

the appearance of steep, tall berms 

(Figure 3) are frequently, if not 

always, sites of water control 

structures and should be field 

verified. The bottom of the control 

structure could represent the 

connection threshold; however, other 

higher-elevation locations may exist

within the channel (Figure 3). Once 

connection thresholds were 

identified, polygons were drawn 

around each location (Figure 3). 

Because the LiDAR and bathymetric 

point data were contained within 

multipoint files, individual point 

elevations could not be displayed. Thus, LiDAR and bathymetric point files were clipped by the

connection-threshold polygons, returning only the points within each polygon. The X, Y, Z data 

were added to the subsequent point file. The points were then symbolized by their Z values to 

identify the elevation water must exceed to pass through the area (connection threshold) 

(Figure 3).

For sites with only bathymetric transect data, a series of aerial imagery collected at different river 

stages was used to identify connecting-channel locations. The elevations of the bathymetric 

transect points falling within these channels were studied to determine the approximate 

connection-threshold elevation. For some connecting channels with no associated bed elevation 

Figure 3. Detail of connecting channel, berm with culvert, 

connection threshold and its elevation, and 

LiDAR points clipped from the LiDAR multipoint 

file for Graveyard Blue Hole.
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data, field observations of connectivity at specific gage heights were used to establish the 

connection threshold. 

Connection Frequency. Water surface elevation at the Helena, AR, gage; the average river

slope between Helena at RM 663.1 and Friar Point at RM 652.5; and connection-threshold 

elevations were used to determine timing and frequency of surface-water connections between 

waterbodies and the Mississippi River main channel. Timing and frequency are approximations 

because they rely on a comparison of a onetime measurement of the connection-threshold 

elevation; in reality, the connection-threshold elevation may change over time. Connectivity is 

ecologically relevant in conservation biology. Infrequent connection promotes unique species 

assemblages, increasing overall ecosystem diversity. A more frequent single surface connection

allows aquatic nutrients and organisms to move between the river’s main channel and floodplain 

waterbodies. Two or more connections provide flow-through conditions, flushing accumulated 

suspended organic matter and equalizing water quality. Surface connectivity was quantified by

the following metrics: 

1. The approximate percent of time the site was connected from 2000 to 2015

2. The study site’s connection status on the sampling day

3. The number of days prior to the sampling day since the site had been connected 

4. The number of days connected during this connection event

A measure of slope was needed to account for north to south elevation change; the LMR at Cairo 

is approximately 315 ft above sea level (asl) and 0 ft asl at its mouth. The slope between Helena 

and Friar Point and Helena and Fair Landing was calculated at four discrete discharges and the 

average slope chosen. This method does not account for daily variation in water surface slope. A 

more accurate method that does account for daily changes is to use daily readings from two 

different gages in close proximity or that bracket the project area. This method was not used 

because there was no second suitable gage. Nearby gages had long periods with no readings or 

were downstream of tributaries whose inputs change the water surface slope of the river. The 

analysis period of 2000–2015 was chosen because it encompasses a full range of hydrologic 

conditions (drought to flood years) and stage discharge comparisons indicate a relatively stable 

river bed at the study site during this time. 

Helena gage water surface elevations were downloaded from rivergages.com and converted from 

NGVD29 to NAVD88 with the VERTCON (2015) conversion of −0.151 ft. Water surface 

elevations for days with no data were determined by averaging the previous and subsequent day’s 

data. The slope, river miles, and the Helena gage were used to convert the connection-threshold 

elevation to an elevation at the Helena gage. For example, the Helena gage is located at RM 663.1,

and river water enters Mellwood Lake at RM 625.8. Thus Mellwood’s connection threshold can 

be converted to a Helena stage by converting 37.3 miles to feet, multiplying by the slope, and 
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adding the value to the connection threshold. This value is then compared to Helena gage daily

water surface elevations by using tables and functions within Microsoft Excel to calculate the 

connectivity metrics. Connectivity metrics were then validated by comparing predicted 

connection dates with observed connection dates recorded during field sampling and by HOBO®

U20L-01 data loggers (Onset Computer Corporation, Bourne, MA) deployed at a subset of sites.

SUMMARY: Connectivity conservation is a global initiative to create or rehabilitate corridors 

between areas of high biodiversity (Crooks and Sanjayan 2006). The approach outlined in this 

document is the first step in understanding connectivity thresholds and frequency between the 

main channel of the Mississippi River and its floodplain. LiDAR and bathymetric data were used 

to create a nearly continuous bare-earth model of a 20-mile reach around Island 63. This model 

was used to find channels that connected floodplain waterbodies to the main channel of the 

Mississippi River. Connection thresholds were then located, a river mile assigned, and the 

frequency of connection determined using gage data. Study results will provide quantifiable 

metrics to rank planning projects, to evaluate current conditions, and to forecast future conditions,

aiding in the management and enhancement of riverine and floodplain biodiversity. Monitoring 

and improving connectivity will also satisfy certain terms and conditions of USACE’s 

Conservation Plan in the LMR (Killgore et al. 2014), inform reasonable and prudent measures in 

the U.S. Fish and Wildlife Service’s (USFWS) Biological Opinion (USFWS 2013), and support

preparation of environmental assessments. Future studies of the location, elevation, and frequency 

of connection on the remaining connected Mississippi floodplain waterbodies at a district- or 

division-wide scale could document whether an array of connectivity is being maintained and 

prioritize areas to improve conservation corridors in the LMR. 

ADDITIONAL INFORMATION: This Mississippi River Geomorphology and Potamology 

Program (MRG&P) Technical Note was prepared by Amanda J. M. Oliver, OSE Jaya Corporation, 

and Catherine E. Murphy, Charles D. Little, Jr., and K. Jack Killgore, U.S. Army Engineer 

Research and Development Center, Vicksburg, MS. The study was funded by MRG&P. Additional 

information pertaining to MRG&P may be obtained from Dr. Barb Kleiss, Mississippi Valley 

Division. This Technical Note should be cited as follows:

Oliver, A. J. M., C. E. Murphy, C. D. Little, Jr., and K. J. Killgore. 2016. Measuring 

Connectivity of Floodplain Waterbodies to the Lower Mississippi River. MRG&P Tech 

Note No. 1. Vicksburg, MS: U.S. Army Engineer Research and Development Center.
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