In the ocean, the performance of active sonar systems used for object detection and seafloor characterization can be affected when the acoustic properties of the seafloor change due to near-bottom hydrodynamics and biological activity. Determining the dominant environmental mechanisms and corresponding time scales that regulate seafloor scattering will increase our understanding of the performance of these remote-sensing applications. To this end, a high-frequency active acoustic system (operating at 38 kHz, 70 kHz and 200 kHz), a wave-sensing CTD, and a stereo camera were deployed on the seafloor in a series of experiments lasting from two weeks to five months. Seafloor scattering measurements were obtained in two shallow water locations in New Hampshire, USA: a wave-dominated site and a tidal current dominated site. Daily and weekly trends in mean scattered levels and the mechanisms causing their temporal variability are discussed. The temporal change in scattering as a function of angle is compared to the small-slope approximation model where seafloor roughness estimates were obtained using stereophotogrammetry.