Abstract A study of the phytoplankton community and water column chemistry in Kaneohe Bay, Oahu, Hawaii, before and after the diversion of secondary treated sewage from the bay has shown that changes in total nutrient concentrations in the water column cannot be accurately predicted without taking into account water column-benthos interactions. During the first year after sewage diversion, the decomposition of about 400 tonnes of benthic organisms, primarily filter feeders, resulted in water column dissolved organic nitrogen and phosphorus concentrations roughly an order of magnitude higher than those expected in the absence of such interactions. The biomass of phytoplankton appears to have been N limited both before and after sewage diversion, with internal nutrient recycling accounting for 70–99% of phtyoplankton nutrient uptake. Both the biomass and growth rate of the phytoplankton declined as a result of the sewage diversion, with post-diversion growth rates evidently well below nutrient-saturated values. Since the principal stresses on the bay's coral reef community as a result of the sewage discharges appear to have resulted from the elevated concentrations of plankton in the water, various measures of seston concentration appear to be the most ecologically significant indicators of nutrient enrichment in this system.