In order to quantify the fate of nutrients originating from shrimp pond waste, mass balances of carbon (C) and nitrogen (N) were compared from a mangrove creek that received shrimp farm effluent to those in an adjacent control creek that did not receive effluent. The annual C input from the shrimp farm exceeded carbon metabolism in creek water and sediments, indicating high sedimentation and burial of excess organic material in the upper reaches of the effluent creek. The rate of natural N flow was small compared with the rate of N supply from pond effluent. Ammonium uptake in creek water and sediment denitrification each accounted for less than 10% of the annual effluent N supply. Immediately downstream from the farm discharge point, mineralisation and release of dissolved inorganic and organic N from the sediments were not greatly enhanced compared to the control creek, despite 25% of the annual N supply and 10% of the annual C supply depositing in proximity to the discharge point. Further downstream, rapid bacterial growth and high rates of primary production were controlled by very high micro-zooplankton grazing rates. The remaining nutrients were exported from the upper reaches to the seaward end of the effluent creek via tidal flushing. On an annual basis, the upper reaches of the creek appeared to mineralise only a small fraction of the nutrients derived from the shrimp farm wastes. However, discharge of pond waste C and N during shrimp harvest periods did not cause eutrophication further downstream, probably due to a combination of physical mechanisms (intensive tidal flushing) and biological nutrient transformations by pelagic microbes and their subsequent grazing by micro-zooplankton and fish.