1. Large rivers in the central United States experience a variety of ecological interactions. Both short- and long-term temporal changes affect both fish and zooplankton communities in rivers. Variation in diel patterns of predation could affect differences of behavior in prey. Long term temporal changes across seasons can lead to different areas of rivers providing growth or costing energy. Spatial changes also affect habitat quality and behaviors of the aquatic organisms within large rivers. Spatial variation can be dynamic and occur between longitudinally connected habitats or vary through different sections of the reach and can also change seasonally. 2. Invasive species have major economic and ecological impacts. In aquatic ecosystems, plankton are the base of the food web and a planktivore invader can cause major ecological disruptions. The Wabash River is a large free flowing river with a variable hydrology, which causes dramatic changes in habitat availability through time. Therefore, habitat usage, quality, and availability may differ for native and invasive species through time. The objectives of this study were to assess how habitat quality changes in a large, flashy, free-flowing river over time, and to compare the quantity and overlap of quality macrohabitat for invasive and native fish. Growth rate potential (GRP) was used to quantify habitat quality for Silver Carp (Hypophthalmichthys molitrix; invasive) and Gizzard Shad (Dorosoma cepedianum; native). To calculate GRP, bioenergetic models were used with monthly observations of food abundance (zooplankton, phytoplankton, and detritus), water temperature, dissolved oxygen, and water velocity of various habitat types from the Wabash River’s confluence with the Ohio River upstream to Terre Haute, Indiana, approximately 215 river miles. Negative GRP for both Silver Carp and Gizzard Shad occurred during spring and most of summer. However, in the fall, the majority of the river had a positive GRP for both species. Reduced flows and increases in food abundance were the cause for the switch from negative to positive GRP. There was a high degree of spatial overlap in positive GRP areas between Silver Carp and Gizzard Shad, suggesting that there is a high degree of competition. Acoustically tagged Silver Carp selected for areas predicted to have a positive GRP from the model presented in the study. This model showed that regulation of flows in hydrologically altered systems could potentially lower the impact of Silver Carp in those systems. With Silver Carp selecting for predicted habitats, a bioenergetics model can be used to inform commercial fishers where to focus effort to maximize catch.3. Temporal changes in rivers tend to be quantified at broad seasonal scales. However, river conditions including water flow, water temperature, dissolved oxygen, and availability of zooplankton prey may change daily. In large rivers, these conditions may change in a diel fashion between backwater and main channel habitats. To assess diel changes in the Illinois River, zooplankton, paired with mobile hydroacoustic surveys for fish were sampled from three main channel and three off-channel sites in the LaGrange reach every four hours in a twenty-four-hour period at different depths between October 22 and 26, 2018. Water depth, water temperature, water velocity, and fish (planktivore and nonplanktivore) densities were quantified during each sampling time. Water temperature and water velocity differed between the two habitat types. Water temperature was higher and water velocity was lower in the off-channel. Water temperature was colder in the morning in both the main channel and off-channel. Water velocity did not change throughout the day. The majority of the zooplankton community was comprised of rotifers which were less mobile than larger taxa and did not migrate. When evaluating the more mobile, large body zooplankton, time and depth affected copepod density in off-channel environments, where the deeper depth had a higher copepod density than the shallower depth. In contrast, only time of day affected off-channel cladoceran density, where densities increased at night. Fish did not exhibit diel patterns and the off-channel habitat had a higher density. The most likely mechanism behind the diel movements of the large bodied zooplankton was predation by planktivorous fish. The present study suggests that connections to the off-channel habitats in large rivers will promote quality habitat for both zooplankton and fish.

Large scale ecosystem restoration is an important societal issue because significant risks, costs, and benefits can accrue on large landscapes. It is important to understand baseline ecosystem conditions, existing condition, and to the extent possible estimate ecosystem response to alternative management scenarios. Incorporating ecosystem process and function into restoration planning and implementation will make ecosystem restoration projects sustainable. The Upper Mississippi River System is an excellent case study for such issues because it is an important, multiple-use ecosystem with significant ongoing investment in ecosystem, agri-system, and navigation system management. Large-scale geomorphology, hydrology, and land cover information was compared among presettlement, contemporary, and potential future reference conditions to examine ecosystem state and evaluate mechanisms responsible for ecosystem condition. The UMRS was scaled by physiographically similar characteristics into large floodplain reaches several hundred river miles in length, geomorphic reaches 50 to several hundred miles, and a mile-by-mile segmentation of the river floodplain extent. Ecologically relevant geomorphic classes were devised from existing data and evaluated by river reach to characterize presettlement geomorphology, and dams and levees were superimposed to reflect the altered hydrogeomorphology of the contemporary ecosystem. A pre- and post-impact Indicators of Hydrologic Alteration river stage analysis evaluated dam impacts, and pre-dam and post-dam aquatic habitat class distribution was compared. A floodplain inundation simulation analysis provided new information on the potential spatial distribution of frequent floods. Land cover data available for presettlement and modern reference periods were compared at several spatial scales. Multivariate analyses evaluated land cover characteristics among geomorphic reaches, as well as to assess the influence of hydrogeomorphic drivers on land cover for presettlement and contemporary reference periods. The objective of this research was to clearly delineate the divergence of environmental conditions among reference periods to evaluate which drivers need to be, and can be, altered to change ecosystem state. Hydrogeomorphic response to development indicates several restoration objectives that are appropriate system-wide and others that are best suited to specific river reaches. Similar data sources are available for much of the rest of the United States through the Public Land Survey and engineering surveys of any significant civil works projects.

Understanding energy fluxes within and between floodplain water bodies, and between rivers and their floodplains is essential for comprehending the dynamics of modern, altered river systems. Floodplain aquatic invertebrates may move between habitats deliberately (through emergence and dispersal) or through passive transport during flooding. This movement may represent a significant flux of energy and an essential food web subsidy. I assessed the usefulness of the stable isotopes of hydrogen and oxygen (D and 18O respectively) for identifying the origins and movements of macroinvertebrates in Mississippi River floodplain water bodies. I sampled water and invertebrates from the Mississippi River, intermittent and permanent floodplain wetlands, and tributaries during 2007 and 2008. Results showed consistent relationships between δD and δ18O signatures in invertebrate tissues and their home water bodies. I also investigated whether δD and δ18O could be used as a multivariate "fingerprint" to trace a captured invertebrate back to its environment of origin. Results showed that δD can be a useful tracer of the movement of floodplain invertebrates in some cases, although δ18O is likely not suitable for that purpose.