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Rivers are complex, dynamic natural systems. The performance of river ecosystem functions, such as habitat availability and sediment transport, depends on the interplay of hydrologic dynamics (flow) and geomorphic settings (form). However, most river restoration studies evaluate the role of either flow or form without regard for their dynamic interactions. Despite substantial recent interest in quantifying environmental water requirements to support integrated water management efforts, the absence of quantitative, transferable relationships between river flow, form, and ecosystem functions remains a major limitation. This research proposes a novel, process-driven methodology for evaluating river flow-form-function linkages in support of basin-scale environmental water management. This methodology utilizes publically available geospatial and time-series data and targeted field data collection to improve basic understanding of river systems with limited data and resource requirements. First, a hydrologic classification system is developed to characterize natural hydrologic variability across a highly altered, physio-climatically diverse landscape. Next, a statistical analysis is used to characterize reach-scale geomorphic variability and to investigate the utility of topographic variability attributes (TVAs, subreach-scale undulations in channel width and depth), alongside traditional reach-averaged attributes, for distinguishing dominant geomorphic forms and processes across a hydroscape. Finally, the interacting roles of flow (hydrologic regime, water year type, and hydrologic impairment) and form (channel morphology) are quantitatively evaluated with respect to ecosystem functions related to hydrogeomorphic processes, aquatic habitat, and riparian habitat. Synthetic river corridor generation is used to evaluate and isolate the role of distinct geomorphic attributes without the need for intensive topographic surveying. This three-part methodology was successfully applied in the Sacramento Basin of California, USA, a large, heavily altered Mediterranean-montane basin. A spatially-explicit hydrologic classification of California distinguished eight natural hydrologic regimes representing distinct flow sources, hydrologic characteristics, and rainfall-runoff controls. A hydro-geomorphic sub-classification of the Sacramento Basin based on stratified random field surveys of 161 stream reaches distinguished nine channel types consisting of both previously identified and new channel types. Results indicate that TVAs provide a quantitative basis for interpreting non-uniform as well as uniform geomorphic processes to better distinguish linked channel forms and functions of ecological significance. Finally, evaluation of six ecosystem functions across alternative flow-form scenarios in the Yuba River watershed highlights critical tradeoffs in ecosystem performance and emphasizes the significance of spatiotemporal diversity of flow and form for maintaining ecosystem integrity. The methodology developed in this dissertation is broadly applicable and extensible to other river systems and ecosystem functions, where findings can be used to characterize complex controls on river ecosystems, assess impacts of proposed flow and form alterations, and inform river restoration strategies. Overall, this research improves scientific understanding of the linkages between hydrology, geomorphology, and river ecosystems to more efficiently allocate scare water resources for human and environmental objectives across natural and built landscapes.