Two high-resolution bathymetric and acoustic backscatter sonar surveys were conducted along the energetic emergent inner shelf of northern Monterey Bay, CA, USA, in the fall of 2005 and the spring of 2006 to determine the impact of winter storm waves, beach erosion, and river floods on biologically-important siliclastic bedrock reef habitats. The surveys extended from water depths of 4 m to 22 m and covered an area of 3.14 km2, 45.8% of which was bedrock, gravel, and coarse-grained sand and 54.2% was fine-grained sand. Our analyses of the bathymetric and acoustic backscatter data demonstrates that during the 6 months between surveys, 11.4% of the study area was buried by fine-grained sand while erosion resulted in the exposure of bedrock or coarse-grained sand over 26.5% of the study area. The probability of burial decreased with increasing water depth and rugosity; the probability of exhumation increased with increasing wave-induced near-bed shear stress, seabed slope and rugosity. Much of the detected change was at the boundary between bedrock and unconsolidated sediment due to sedimentation and erosion burying or exhuming bedrock, respectively. In a number of cases, however, the change in seabed character was apparently due to changes in sediment grain size when scour exposed what appeared to be an underlying coarser-grained lag or the burial of coarser-grained sand and gravel by fine-grained sand. These findings suggest that, in some places, (a) burial and exhumation of nearshore bedrock reefs along rocky, energetic inner shelves occurs over seasonal timescales and appears related to intrinsic factors such as seabed morphology and extrinsic factors such as wave forces, and (b) single acoustic surveys typically employed for geologic characterization and/or habitat mapping may not adequately characterize the geomorphologic and sedimentologic nature of these types of environments that typify most of the Pacific Ocean and up to 50% of the world's coastlines.