Natural streams typically have highly complex flow patterns. Velocity gradients, circulation zones, transverse flows, and other flow patterns are created in the presence of topographic features (e.g. exposed boulders, bars). How flow complexity influences a stream's ecological health and morphological stability, as well as how flow complexity responds to changes in hydrologic conditions, is poorly understood. One-dimensional (1-D) hydraulic models and two-dimensional (2-D) models that do not explicitly incorporate meso-scale topographic features are not capable of adequately reproducing the flow patterns found in channels having complex topography. Moreover, point measurements of depth and velocity, which are used to describe hydraulic conditions in habitat suitability studies, cannot be used to characterize spatially varying flow patterns of biological importance. A general methodology for incorporating meso-scale topography into 2-D hydraulic models is presented. The method provides a means of adequately reproducing spatial flows of interest to riverine researchers. The method is developed using 2-D model simulations of a reach of the North Fork of the Feather River in California. Specifically, the site is modeled with and without bathymetry data on exposed boulders found within the site. Results show that the incorporation of boulder topography and an adequately refined mesh are necessary for reproducing velocity gradients, transverse flows, and other spatial flows. These simulations are also used to develop and evaluate three spatial hydraulic metrics designed to distinguish between locations having uniform and non-uniform flow conditions. The first two metrics describe local variations in energy/velocity gradients, while the third metric provides a measure of the flow complexity occurring within an arbitrary area. The metrics based on principles of fluid mechanics (kinetic energy, vorticity, and circulation) can be computed in the field or with 2-D hydraulic model results. These three metrics, used in conjunction with detailed 2-D hydraulic model results, provide engineers, biologist, and water resource managers a set of tools with which to evaluate the importance of flow complexity within rivers. A conceptual model describing how such a tool can be used to help design channels being restored, better evaluate stream habitat, and evaluate how hydrologic changes in a watershed impact hydraulic conditions and concomitant habitat conditions is provided. / Ph. D.