Many warmwater streams in the midwestern United States have been negatively influenced by human land-use practices. From Jun. through Aug. 2002 and 2003, tributaries (n  =  50) of the upper Wabash River basin, Indiana, were sampled to investigate ecosystem health and integrity. Stream fish and macroinvertebrates were sampled along with in-stream habitat according to National Water-Quality Assessment Program protocols to examine relationships among fish community structure, benthic macroinvertebrate assemblages, physical-habitat complexity and water chemistry under varying land-use practices. Stream fish abundance was best explained by in-stream habitat quality (QHEI), watershed area and the amount of forested land use upstream of each sampling site. Overall index of biotic integrity (IBI) scores were low (mean  =  35.58; range, 20 to 52), and varied predictably by riparian land-use type. The abundance of benthic macroinvertebrate taxa was best explained by the substrate QHEI metric (λ  =  0.24; P  =  0.005). Macroinvertebrate community index (ICI) scores showed more variability than IBI scores (mean  =  20.40; range, 0 to 36). In-stream habitat quality (QHEI) was directly related to riparian land-use practices. Forested sites had higher QHEI scores than fallow field and agricultural sites due to increased habitat heterogeneity, large-woody debris loading and larger substrate sizes. The best model for predicting IBI scores incorporated both watershed and reach-scale variables combining slope and erosion power with maximum depth, percent canopy closure, percent fine substrates, degree of channelization and LWDI (r²  =  0.24; adjr²  =  0.19). Reach-scale variables (i.e., QHEI score, stream width, the proportion of unstable banks and percent fine substrates) best predicted ICI scores (r²  =  0.69; adjr²  =  0.66). Based on these results, we recommend that resource managers incorporate both biotic and abiotic factors at various temporal and spatial scales to predict the effects of land-use practices on community health in agriculturally dominated, warmwater streams.