Abstract There is a growing body of research that examines bedrock channels. Despite this, biotic-abiotic interactions remain a topic mostly addressed in alluvial systems. This research seeks to identify patch-scale hydro-geomorphic factors operating at the patch-scale in bedrock shoals of the Cahaba River (AL) that help determine the distribution of the emergent aquatic macrophyte, Justicia americana. Macrophyte patch density (number of stems/m2) and percent bedrock void surface area (rock surface area/m2 occupied by joints, fractures, and potholes) were measured (n = 24) using stem counts and underwater photography, respectively. One-dimensional hydrologic modeling (HEC-RAS 4.1.0) was completed for one cross-section within a shoal to examine whether velocity and channel depth are controlling variables for macrophyte patch density. A Pearson's Correlation test between bedrock surface void area and stem density demonstrated a statistically significant positive correlation (r=.665, p=0.01). Results of an independent t-test between the velocity and depth model outputs for within and outside plant patches showed a significant difference in average velocity (p =0.011) and depth (p = 0.001) between the two types of locations across discharges, ranging from 7 m3/sec to 226 m3/sec. These results suggest that the amount of void space present in bedrock surfaces and localized depth and velocity help control the macrophyte patch density, and by extension, the distribution of macrophytes in bedrock shoal complexes. The utility of geomorphology in explaining patch-scale habitat heterogeneity in this study demonstrates potential to use geomorphology to explain macrophyte habitat heterogeneity at reach and system-scales and highlights the need for more research that helps understand biotic-abiotic interactions in bedrock fluvial systems.