FISH ASSEMBLAGES RESPOND TO HABITAT AND HYDROLOGY IN THE WABASH RIVER, INDIANA J. PRITCHETT AND M. PYRON* Department of Biology, Aquatic Biology and Fisheries Center, Ball State University, Muncie, Indiana, USA ABSTRACT Detailed relationships between fish assemblages and habitat and hydrology variation are largely unknown for large rivers. We evaluated hydrology, habitat variation and fish assemblages at 28 sites on the Wabash River, Indiana, USA, during 2005–2008. We calculated hydrologic variation with the Indicators of Hydrologic Alteration software and tested for temporal hydrologic effects on habitat variation of substrate particle size, water depth and water velocity by reducing data into principal component axes that were tested for differences among years with ANOVAs. We then tested for effects of habitat and hydrology variation on fish assemblages with canonical correspondence analysis. These analyses showed significant relationships between hydrologic variation and local habitats, and hydrology and habitat variables had significant relationships with fish assemblage structure. Our Mantel tests resulted in significant concordance among hydrology, local habitat variation and fish assemblage structure, suggesting associations of these variables. These results supported strong connections for hydraulic control over habitat variation and subsequent effects on fish assemblages. Copyright © 2011 John Wiley & Sons, Ltd. key words: habitat variation; large river; multivariate analysis; hydrologic alteration Received 8 December 2010; Revised 4 March 2011; Accepted 18 March 2011 INTRODUCTION The distribution of physical stream attributes is controlled by geomorphology and climate patterns (Frissell et al., 1986). At regional scales, geology and topography control meandering patterns and riffle‐pool development and locations. At a local scale, the hydrologic regime results in scouring and deposition patterns, creating a variety of available substrates by transporting and distributing sub- strata (Leopold et al., 1964). Decreased flow in a local reach results in deposition of smaller sediment particles, whereas local reaches with increased flow have larger sediments (Wetzel, 2001). The resulting habitat structure, including substrate particle size, influences the distribution of aquatic organisms. The abundance and distribution of riverine biota are controlled largely by variation in physical habitat character- istics (Meffe and Sheldon, 1988; Poff and Ward, 1990; Poff and Allan, 1995; Hitt and Angermeier, 2008; Neebling and Quist, 2010). Habitat characteristics that aquatic organisms respond to include substrates, woody debris and local hydraulics (Bilby, 1984; Resh et al., 1988; Allan, 1995; Walters et al., 2003; Kennard et al., 2007). For example, fish assemblages respond to substrate size distribution patterns (Hitt and Angermeier, 2008). Larger, more stable substrates provide cover for fish as well as habitat for aquatic insects, whereas the deposition of fine sediments results in decreased species abundance (Gurtz and Wallace, 1984; Allan, 1995; Wood and Armitage, 1997; Matthews, 1998). Ecological processes in streams are further structured by hydrologic regimes that have the potential to be altered from a natural flow regime (Poff and Ward, 1990; Poff et al., 1997). Poff and Allan (1995) found that altered hydrologic regimes impacted the occurrence of fish species based on tolerance categories. Sites with increased hydrologic variation were associated with generalist species although specialists were found in stable environments. Several biologically relevant hydrologic variables are predictors of how riverine biota will be influenced by specific hydrology patterns (Richter et al., 1996). However, the mechanisms for hydrologic variation impacting fish assemblages are mostly indirect, through effects on habitat variables. Multiple studies have found that fish assemblages vary with substrates and/or hydrology (Poff and Allan, 1995; Smith and Kraft, 2005; Mueller and Pyron, 2010). Although stream assemblages have been examined for these relation- ships (Gorman and Karr, 1978; Berkman and Rabeni, 1987; Meffe and Sheldon, 1988; Poff and Allan, 1995), few studies tested for effects of hydrology and detailed habitat attributes on fish assemblages of large rivers (Neebling and Quist, 2010). The first objective of this study was to identify *Correspondence to: M. Pyron, Department of Biology, Aquatic Biology and Fisheries Center, Ball State University, Muncie, Indiana 47306, USA. E‐mail: mpyron@bsu.edu RIVER RESEARCH AND APPLICATIONS River Res. Applic. (2011) Published online in Wiley Online Library (wileyonlinelibrary.com) DOI: 10.1002/rra.1528 Copyright © 2011 John Wiley & Sons, Ltd.