Reservoir releases for generating power need to be reconciled with efforts to maintain healthy ecosystems in regulated rivers having irregular channel topography. Fluctuating, complex flow patterns near river obstructions such as boulders and large woody debris provide unique habitat for many aquatic organisms. Numerical modeling of the flow structures surrounding these obstructions is challenging, yet it represents an important tool for aquatic habitat assessment. Moreover, efforts for modeling the morphologically and biologically important transient flows, as well as quantifying their impacts on physical fish habitat during the unsteady-flow period remain rare. In this dissertation, the ability of two- (2-D) and three-dimensional (3-D) hydraulic models to reproduce the localized complex flow features at steady base and peak flows is examined first. The performance of the two hydraulic models is evaluated by comparing the numerical results with measurements of flow around a laboratory hemisphere and boulders located at a reach of the Smith River in Virginia. Close agreement between measured values and the velocity profiles predicted by the two models is obtained outside the wakes behind these obstructions. However, results suggest that in the vicinity of theses obstructions the 3-D model is better suited for reproducing the circulation flow behavior favored by many aquatic species over a broad range of flows. Further, time-dependent flow features affecting channel morphology and aquatic physical habitat are investigated using the numerical models for the same reach in the Smith River. Temporal variation measurements of water surface elevation and velocity profile obtained in the field during a reservoir release are in good agreement with the numerical results. A hypothetical "staggering" flow release scenario simulated by the 3-D model leads to reduced erosional area and longer refugia availability for juvenile brown trout during hydropeaking. Finally, an unsteadiness parameter β is proposed for determining whether an unsteady flow regime can be either modeled using a truly dynamic flow approach or a quasi-steady flow method. / Ph. D.