This is a study of the interaction effects of the dual frequency (210 and 33 kHz) backscatter signal with seafloor sediment and benthic biota along a transect in water 27–83 m deep offshore of the Goa region of India’s central west coast. Estimation of the power law exponent using seafloor topographic data provided equivalent values even when using dual high-frequency systems for different grain-size sediments. Backscatter signals corrected from system-related gain, etc., reveal better correlations with sedimentary and benthic parameters than the estimated coherence parameters (using echo peaks). Statistically, correlations are significant for the 210 kHz backscatter signal with sand and calcium carbonate (CaCO3) sediment content. Also, correlations are higher for macrobenthic biomass (wet weight) and population density with a 210 kHz backscatter strength, emphasizing the dominant seawater-seafloor interface scattering process. For 33 kHz backscatter strength, the absence of such correlations indicates a different scattering processes, i.e. dominant sediment volume scattering attributable to the comparatively lower signal attenuation. Additionally, to validate the results, the backscatter signal from other locations in the vicinity of this transect were considered.