The goal of this thesis is to advance our knowledge of stream ecosystems by evaluating how physical habitat, especially large woody debris (LWD), affects fish populations and particulate matter retention in streams of the Upper Peninsula of Michigan (UP). Even though streams in the UP had relatively low amounts of LWD compared to other regions in North America, LWD still influenced physical habitat variables. In UP coldwater streams, trout populations were positively related to LWD amounts whereas the total fish community related more to the overall stream habitat conditions (e.g., stream area and volume, substrate size, pool habitat, temperature). All streams were highly retentive of coarse particulate matter, which was strongly influenced by discharge, current velocity, and debris dams. On average, all particle types traveled less than 7 m. Overall, my research provides an ecological framework for the management of physical habitat in low-gradient streams of the upper Midwest.