Shrimp aquaculture is a major industry in south east Asia and the Americas but there is growing international concern about the negative impacts of farm discharges on coastal and estuarine ecosystems. This study determined the effect of high nitrogen loadings on the dominant pathways of nitrogen transformation in intensive shrimp ponds. The aim was to provide a scientific basis for reducing dietary nitrogen waste and hence minimizing the environmental effects due to the discharge of wastewater into adjacent waterways. Using 15N-enriched artificial food fed to shrimp, it was determined that only 20 to 30% of the dietary nitrogen consumed by shrimps was retained after two weeks. The remainder entered the pond water column and sediment. Some shrimp excretory products from feeding, namely ammonium and urea, were rapidly assimilated by the plankton. Other larger molecular weight organic compounds resulting from shrimp feeding were not readily utilized by the plankton or bacterial communities and accumulated in the water column. Particulate waste products from feeding and other pond detritus were deposited on the sediment floor creating anoxic conditions. Ammonium fluxes from the sediment were high resulting in the accumulation of ammonium in the water column. Much of the loss of nitrogen was via water discharges with little nitrogen removal by denitrification. The results of this study were synthesized into a conceptual model of nitrogen transformation. This highlights the major pathways; namely rapid cycling of dietary nitrogen through the ammonium pathway and slower cycling of dietary nitrogen through the dissolved organic nitrogen pathway. The model provides a mechanism to target research into the most effective methods to improve water quality and reduce waste nitrogen discharges. More generally, it provides information on the effect of high nitrogen loads on ecological processes that is applicable to studies in natural systems. Based on the model, there appears to be considerable scope to reduce waste nitrogen discharges to the natural environment by enhancing pond ecological processes, and by improving feeds and feeding strategies.