Heterogeneity in physical habitat may be a key requirement for some riverine species to succeed in a naturally fluctuating flow environment; however, methods to quantify habitat heterogeneity in a manner relevant to the ecology of in-stream species are lacking. Spatial heterogeneity indices from landscape ecology are often applied on large-scale terrestrial landscapes to objectively quantify habitat variability, and may be similarly useful at the smaller river reach scale. Specifically, spatial indices calculated for a river reach \textquoteleftlandscape\textquoteright, when compared to species abundance to determine which indices are most ecologically significant, may reveal patterns in habitat preference as well as provide an objective way to quantify heterogeneity. To explore this concept, I evaluated the geomorphic features on four creeks tributary to the South and Middle Yuba Rivers, Nevada County, California known to support populations of Foothill Yellow-legged Frog (Rana boylii), a river-breeding amphibian. Using FRAGSTATS, I calculated four spatial indices quantifying spatial composition (patch shape, diversity, richness and evenness) and two indices quantifying spatial configuration (contagion and interspersion) for each study reach, and compared them with relative frog abundance. Results from multiple linear regression analyses showed indices of spatial composition correlated well with frog abundance, while indices of spatial configuration were not significant. The most significant regression model contained only Shannon\textquoterights Diversity Index as the best predictor of frog abundance such that as the diversity in geomorphic units throughout the reach increased, relative frog abundance increased. These findings, when considered with data from previous studies, indicate R. boylii selects stream reaches with increased geomorphic complexity that provide habitats suitable to each lifestage, habitats with multiple functions (e.g. cover, forage, basking and breeding) and a greater variety of refugia as flows fluctuate throughout the season. In summary, spatial heterogeneity indices were useful in quantifying geomorphic habitat heterogeneity at the river reach scale, and when related to R. boylii abundance, provided insight to aspects of their life history strategy. These types of indices, when shown to be ecologically meaningful to a particular aquatic species of interest, could be used to quantify habitat in river restoration or conservation practices.