Elucidation of habitat and resource use patterns is important for facilitating sustainable management of fisheries. Discrete habitats in large aquatic ecosystems may offer distinct resources and differentially affect performance. Movement of organisms and organic materials links these habitats and potentially leads to spatially complex trophic pathways between basal resources and consumers. Habitat and resource use are commonly explored via two common methods: stable isotopes and morphometric analysis. The first research chapter of this thesis employed both methods to investigate seasonal habitat use of yellow perch Perca flavescensin eastern Lake Michigan and connected waterbodies known as drowned river mouth (DRM) lakes. Landmark-based geometric morphometrics was used to compare shape differences among habitats. Stable isotopes of ambient water, otoliths, and soft tissues were compared to differentiate among habitats. Both methods provided evidence of resident nearshore Lake Michigan fish, resident DRM lake fish occupying the littoral zone, and transient Lake Michigan fish occupying the profundal zone of DRM lakes. The majority of transient Lake Michigan fish moved into the profundal zone of DRM lakes in the fall. These results support previously published genetic data of distinct populations of yellow perch in eastern Lake Michigan and connected waterbodies. The second research chapter of this thesis also employed stable isotopes and morphometric analysis, but to investigate the consistency of resource use of age-0 yellow perch in Saginaw Bay, Lake Huron. These methods served as long-term diet indicators, as compared to short-term stomach contents analysis. Both stable isotopes of soft tissues and morphometric analysis showed spatial consistency in variation among sites. Fish from the two sites closer to the tributary input had higher δ15N values and more fusiform bodies, while fish from the third site further away from the tributary had lower δ15N values and were deeper-bodied. This spatial variation supports stomach content analysis of age-0 yellow perch from a previously published study. δ13C ratios displayed annual variation, and while inconsistent with stomach content analysis, was consistent with available prey items. The findings from this study suggest that young yellow perch in Saginaw Bay have limited movement and forage in a similar area to where they were collected. Previous studies have found discrepancies among indicators and have cautioned generalization of trophic relationships when only relying on a single metric. Agreement between complementary techniques provided additional support to previously-published genetic results and stomach content data, and thereby helped more fully describe habitat use by yellow perch in these systems.