Large-scale habitat preferences of riverine taxa are not always revealed by examining community data. Here, we show how lipid and growth can be used to evaluate hydrologic habitat preferences of fishes resilient to river fragmentation (i.e. species that can tolerate river fragmentation by dams, but not collapse). Lipid content was examined for seven fishes in a major southeastern USA reservoir and its largest lotic tributary over the 5 years. Controlling for effects of sex, size and year of collection, largemouth bass, spotted bass and black crappie had significantly higher lipid in lentic habitat. Conversely, channel catfish and freshwater drum had significantly higher lipid in lotic habitat. There were no significant differences in lipid of bluegill and blacktail shiner between hydrologic habitat types. Fish growth produced concordant results as largemouth bass and spotted bass had significantly faster growth in lentic habitat, whereas channel catfish and freshwater drum had significantly faster growth in lotic habitat. We were also able to document a synchronous spike in lipids of these species in both habitat types during a major drought. We surmise that the spike was driven by enhanced primary production, predator-prey concentration and possibly also reduced reproduction during intense drought. Two conclusions are drawn from this study as a whole. First, long-term lipid and growth observations hold promise for evaluating ecological effects of droughts over long time spans. Second, population characteristics are excellent indicators of habitat preferences and could be used more broadly to elucidate how organisms react to river ecosystem fragmentation and restoration initiatives. Copyright © 2009 John Wiley & Sons, Ltd.