The density and composition of microbial communities of subtidal sandy sediments determines their role in the cycling of nutrients in coastal waters. It has previously been found that sediments disturbed by waves and currents have reduced biomass, greater productivity to respiration (P/R) ratios and a tendency to take up nutrients. Conversely, with shelter and greater biomass, P/R ratios were smaller and nutrients released. This study, in warm temperate waters, examined the consequences of high and low levels of hydrodynamic energy on the microbial community structure and biogeochemistry at two locations at different times of year. Measurements included biomarkers, sediment properties and exchanges of gases and nutrients. Microbial communities were dominated by diatoms and bacteria. Exposed sites, relative to paired sheltered sites, had smaller ratios of bacteria to benthic microalgae (BMA), larger C/N ratios, smaller indices of diagenetic activity, but smaller P/R ratios. The bacteria in exposed sediments exhibited biomass-normalised rates of respiration almost double those in sheltered sediments. This increased activity was most likely fuelled by elevated concentrations of photosynthates, secreted by BMA attached to sand grains. Changes in community composition owing to different levels of disturbance led to shifts in functioning that resulted in consistently small exchanges of nutrients.