In many current hydropower project relicensing studies, instream flow assessment methods are used to evaluate flow effects and proposed flow prescriptions on fish. These techniques may be applicable to other sensitive aquatic species, such as the riverine-breeding Foothill Yellow-legged frog (Rana boylii). Two major components of flow modeling were evaluated as part of this study. First, regional habitat suitability criteria (HSC) were developed using standard univariate and multivariate techniques and the predictive performance and transferability of different HSC methods were evaluated. Based on this evaluation, we recommend that separate creek and river HSC for the Sierra Nevada R. boylii be based on a percentile method. Second, three of the most commonly used instream flow assessment techniques: (1) one-dimensional habitat modeling, (2) two-dimensional hydrodynamic modeling, and (3) expert habitat mapping (judgment-based mapping by species experts), were evaluated. Several flow/habitat relationships were compared among the three modeling methods: total suitable habitat, effective habitat during flow recession, and gradients of suitability during a pulsed flow. Level of effort, scale of resolution, capacity for extrapolation, and specificity of modeling analyses were also qualitatively assessed. A comparison table is provided to aid resource managers in selecting the most appropriate habitat assessment method for R. boylii, given the specific conditions of a hydropower relicensing project. Finally, a website was constructed to provide an updated and publicly accessible synopsis of the status of knowledge on R. boylii, with particular focus on the effects of river regulation on this species. The website provides access to relevant data and literature, tabular summaries of ecology and risks, and a species locality map derived from multiple data sources. Collectively, the elements of the website offer a comprehensive update on the species and may help identify reference populations for monitoring and research.