Understanding the relative influences of biotic and abiotic mechanisms responsible for generating patterns of community diversity remains a fundamental theme in ecology. Although studies have recovered patterns of community structure, the mechanisms responsible for such patterns are often unclear. To better understand assembly mechanisms, I implemented a framework that incorporated phylogeny, morphology, and habitat use data among co-occurring darters (Percidae: Etheostomatinae). Darters are small bodied stream fishes endemic to North America, and due to the high degree of co-occurrence of species in fine scale communities, these systems are ideal for testing assembly mechanisms where inter-specific interactions are plausible. My goals were to identify patterns of habitat use structure, describe mechanisms influential on assembly, and demonstrate the effects of spatial scale on assembly mechanisms within darter communities. To test for mechanisms influential on community assembly, I incorporated metrics of phylogenetic relatedness, habitat use similarity, and morphologic similarity, among co-occurring species within communities at several spatial scales. At the stream site scale, communities showed consistent phylogenetic clustering and habitat use clustering among co-occurring taxa, indicating that habitat filtering (i.e., co-occurrence of species with similar ecological requirements) was the main driver of community assembly; although some degree of evolutionary convergence in habitat use among co-occurring species was found. There were separations in habitat use but these occurred between groups of species rather than among all individual species. Additionally, phylogenetic/habitat use relationships indicated displacement in habitat use among recently diverged taxa. Across multiple spatial scales (from within to across four watersheds) darter communities showed an increase in the prevalence of habitat filtering from fine to intermediate spatial scales, and in two of the four systems there was a signal for habitat filtering at the most broad scale. There was a strong signal for competitive exclusion in only one of the river systems. In conclusion, darter communities showed group separation in habitat use, where similar habitat use is found within groups of species suggesting that competition may not act strongly among individual species within these communities, but rather, competition could act between species groups. Habitat filtering appeared to be the dominate mechanism influencing the assembly of communities, and the relative influence of habitat filtering increased with larger spatial scales. However, the prevalence of simultaneous signal for habitat filtering and competitive exclusion based on trait distributions and phylogenetic patterns further illustrates the complexities of community assembly processes.