Watershed land use alteration and flow extraction influence the physical habitat and geochemical functions of small streams. In two associated studies, I explore stream physical habitat characteristics and nutrient uptake across a range of land use influences (flow extraction, agriculture, and urbanization). In the first study, I examined the effects of flow diversion to fine sediment deposition in a detailed field analysis pairing reaches above and below diversion dams on 13 mountain streams throughout north-central Colorado and southern Wyoming. Diversions are ubiquitous across the American West, yet previous studies on the impact of flow extraction have yielded mixed results. Through application of strict site selection criteria, multiple fine sediment measures, and an intensive sampling scheme, this study found that channels downstream of diversions contained significantly more fine sediment and slow flowing habitat as compared to upstream control reaches. Susceptibility to fine sediment accumulation was associated with decreasing basin size, bankfull depth, and d₈₄, and appears to be magnified in streams of less than 3% slope. In the second study, I investigate physical and hydraulic influences on transient storage and nutrient uptake in small agricultural and urban streams across a gradient of channel conditions and management modifications. Three geomorphically distinct segments on each of two streams were studied in the summer of 2007: one in a Colorado Front Range urban setting and the other in a mountainous agricultural region in north-central Colorado. The urban stream exhibits various levels of stabilization and planform alteration, and the agricultural stream has been subject to historically variable cattle-grazing practices. Reach-scale geomorphic complexity was characterized using highly detailed surveys of channel morphology, substrate, hydraulics, and habitat units. Injections of conservative bromide (Br^-) and non-conservative nitrate (NO₃ ^-) tracers were used to characterize channel processes. Geomorphic characteristics, specifically increased longitudinal roughness and flow depth, were strongly associated with both nutrient uptake and transient storage. Collectively, the studies underscore the primary influence of flow regime on habitat response and nutrient spiraling functions in the context of human influences.