Understanding the geomorphic and hydrologic relationships to instream flora and fauna is essential to successful management of stream and river environments. Broadly, this dissertation research addresses these relationships by investigating hydrologic and geomorphic factors that control imperiled fish habitats in the Etowah River, Georgia. Specifically, I examined factors affecting shoal (i.e., shallow parts of river channels) sediment composition and Podostemum ceratophyllum (riverweed; an aquatic macrophyte). Channel incision caused by channelization or altered hydrology typically reduces habitat complexity and alters sediment composition. Sediment composition and P. ceratophyllum did not differ between incised and slightly incised shoals. Measurements following a flood indicated that bed mobility affects P. ceratophyllum occurrence and length (a correlate of biomass), and may have a stronger effect than channel incision. Proportion bedrock and channel width accounted for 77% of the variation in P. ceratophyllum occurrence among sites, while proportion cobble and basin area accounted for 51% of P. ceratophyllum length variance. Shade, water velocity, and sediment size cumulatively accounted for 47% of the variance in P. ceratophyllum density, 32% in length, and 22% in biomass within sites. Based on the Network Dynamics Hypothesis (NDH), I predicted that tributaries influence mainstem morphology via tributary sediment inputs and that alluvial shoals occur below large tributary confluences. Although tributary basin area and the ratio of tributary to mainstem basin area did not predict shoal occurrence, alluvial shoals were closer to upstream confluences than were other shoal types, indicating an association with tributaries. Shoals near large tributary confluences also contained a larger proportion of gravel and cobble bed sediments and were wider than adjacent, downstream shoals. These geomorphic differences are likely to affect P. ceratophyllum occurrence and length. Monthly and annual monitoring indicated that P. ceratophyllum biomass was highest in late summer and lowest during winter and periods of low stream flow. Among years, P. ceratophyllum presence and length increased as discharge decreased. Precipitation changes and management actions that affect river flows are likely to affect macrophyte occurrence and associated fauna. Cumulatively, these results suggest that landscape or shoal-scale restoration approaches that increase the proportion of coarse sediment in shoals are likely to increase P. ceratophyllum occurrence, length, and persistence.
