Intensive shrimp farming generates high loads of wastewaters that are released along tropical coastlines with potential impacts on the ecosystems. In this study, we used an experimental approach to analyze the behavior of shrimp pond effluents released in the Can Gio mangrove waterways (Southern Vietnam). We incubated shrimp pond effluents (EF), river water (RV), and a mixture of both (MI; 90% RV + 10% EF) in a dark room and measured fatty acid (FA) compositions, C and N concentrations and stable isotopes ratios (δ13C and δ15N) of suspended particulate matter during 16 days. Fatty acid concentrations rapidly decreased in EF with a 50% loss of FA during the first 24 h of the experiment and a 75% loss after 4 days of incubation. Proportions of the FA 18:1ω7 increased in MI during incubation, suggesting that this FA may be used as a tracer of anthropogenic substances release in marine environments.