Rice-shrimp culture systems occur throughout Asia where there are seasonal alterations of fresh and saltwater availability. During the dry season, black tiger shrimp are grown at low densities, and in the wet season, rice, or rice and shrimp are grown together. Previous studies point to issues with suboptimal rice and shrimp production, due, in part, to climatic conditions driving changes in water quality, and pond management practices. However, the availability of natural benthic food supplies for shrimp production is less well studied. This study used a 15N-nitrogen stable isotope tracer added to replicated enclosures within two rice-shrimp ponds to trace shrimp feeding on benthic natural biota. This experiment was conducted in both the wet and dry seasons. The 15N-ammonium rapidly enriched the 15N signature in the particulate organic matter (POM) in the water column, indicative of significant phytoplankton uptake of nitrogen (N). In contrast there was little enrichment of the benthic algae in the same time frame. After 13 d, most of the shrimp in the replicate enclosures had little or no 15N enrichment. This result occurred across both ponds and in both seasons. This suggests that enriched N was not transferred through the benthic food web to the shrimp. The results of the 15N enclosure experiments were combined with biomass estimates of benthic algae and macrobenthos, shrimp growth data, and linked to other parallel studies of water quality and sediment biogeochemistry in the same ponds. Overall, the findings point to inadequate feed stocks for shrimp, and hence the need to consider supplemental feeding with high quality formulated feeds in order to improve growth rates and survival.