The interaction between geomorphology and hydrology forms and governs the type and quality of the habitat upon which biological communities are arranged. Effectively creating links between what controls and impacts stream biota and habitat quality as they relate to geomorphology and hydrology is complex and requires an interdisciplinary understanding. From the hydrologic-geomorphic perspective, knowledge of what dictates and controls fluvial geomorphic processes at the watershed to the reach scale have been identified and mechanisms that initiate changes in sediment supply and/or flow regime resulting in altered stream geomorphic condition have been documented. From the biota-habitat perspective, the knowledge of what biota require for their existence (e.g., thermal regime, water chemistry, habitat for feeding, reproduction, and protection) has been identified and numerous studies have documented an association between instream, near-stream, and watershed land use with changes in water quality, habitat quality, and loss of biological integrity. However, studies often have not always identified the mechanisms and intermediate pathways linking changes in watershed land use to biological impairments. One plausible link is channel stability and the effect on habitat quality. This causal link needs to be more fully explored and documented for Stressor Identification of biological impairments. Biologists, with knowledge related to species traits and habitat requirements may lack geomorphic training; conversely, geomorphologists with an understanding for flow and sediment dynamics may lack an understanding of habitat conditions required by biota. Assessment tools and training that incorporate an understanding of both of these perspectives are needed so that candidate causes and mechanisms associated with a loss in channel stability, habitat quality, and consequently, biological integrity can be identified. Before that can occur, existing habitat and channel stability assessment tools need to be tested and tailored to appropriately rate conditions observed in different regions and stream types so that deviations from the best biologically supporting conditions can be assessed and managed. The objectives of this study were: 1) to test the applicability of a channel stability assessment, namely the Pfankuch Stability Index (PSI) in characterizing stream stability indicators observed in low-gradient streams consisting primarily of fine substrates, 2) to identify key channel stability and habitat quality variables and their level of association with stream health as characterized by a fish index of biotic integrity (FIBI), 3) to explore the level of association between indicators of channel stability and habitat quality, and 4) determine which metrics and variables seem appropriate for assessing and exploring the channel stability and habitat quality linkage in low-gradient streams. Two watersheds were selected in which to pursue these objectives: the Snake River in the St. Croix River Basin and the Redwood River in the Minnesota River Basin. These watersheds contrasted in geology, historical vegetation, and intensity of anthropogenic land use. In total, 28 sites (14 sites in each watershed) were sampled for fish, channel stability, habitat quality, water chemistry, and geomorphic variables including substrate composition, percent stream features, and stream gradient. Watershed land use statistics were estimated in ArcGIS. Statistical tests applied included ANOVA, correlation, linear regression, and multiple linear regression. My results suggest that: 1) modifications to PSI metrics are needed in order to more appropriately rate and characterize indicators of channel stability found in low-gradient streams. Metrics such as rock angularity, brightness, and channel capacity were problematic to score and should be removed or modified. Suggestions for a modified channel stability assessment include: adding metrics that rate the degree of incision and floodplain connectivity, tailoring metric descriptions to conditions observed, incorporating a channel evolution model, and estimating substrate composition, among others. 2) Subjective channel stability assessments can be useful for Stressor Identification of biological impairments. Specifically, metrics associated with the degree of substrate mobility and aggradation explained a significant portion of the variation in FIBI in both watersheds; although, the shape of the association differed between watersheds and should be re-examined in future studies. Habitat quality metrics related to channel morphology, cover, and substrate condition explained a significant portion of the variability in FIBI and were related to channel stability. 3) Other geomorphic variables such as D50 and percent pool and riffle were associated with higher FIBI scores.