In the ocean, the performance of active sonar systems depends on the acoustic properties of the seafloor. Daily to monthly variations in near-bottom hydrodynamics and benthic biological activity may affect seafloor properties which then influence the acoustic response of the seafloor. The dependence of seafloor scatter on evolving environmental parameters was investigated using high-frequency active acoustic systems. Seafloor scattering measurements were analyzed in a series of experiments (two weeks to five months in duration) from downward-looking sonars oriented at 20° grazing angle with respect to the seafloor. Data were obtained in two shallow water locations near Portsmouth, New Hampshire, USA: a wave-dominated site and a site dominated by tidal currents. The bottom type for both sites was gravelly sand. The experimental set-up consisted of a tripod placed on the seafloor equipped with three transducers operating at 38, 70, and 200 kHz, a wave-sensing CTD, and underwater cameras. Scattering strength time series were obtained taking into account the local seafloor slope. Results show that there is variability in scattering strength (both in mean levels and distributions). Large variations often coincided with storm events, suggesting that this variability may be driven by changes in bottom roughness caused by storm-related hydrodynamics.