Fluxes of phosphate across the sediment–water interface have been measured using inhibitors of bacterial activity sterilization and chloramphenicol and a control in order to quantify the influence of bacterial abundance on them. Results show that phosphate concentration in the interstitial water decreased when bacteria were present, in relation to treated aquaria. The measured (Jo) and theoretical fluxes (Jd) of phosphate also were higher when bacterial activity was suppressed. Mass balance calculated for Carbon, Nitrogen and Phosphorus in the sediment revealed a loss of theses compounds when bacterial activity was suppressed, and a net accumulation of Carbon and Phosphorus, and loss of Nitrogen under natural conditions.