Accumulation of nutrients in the sediment under a tilapia cage farm (2.8–4.4% C, 0.26–0.49% N and 0.04–0.26% P) seemed to follow a seasonal pattern, with highest concentrations prior to winter water turnover. However, in April 1994 (and for P also in April 1992) the surface sediment contained significantly higher nutrient concentrations compared to controls. Generally, significantly higher pore water concentrations were found under the cages compared to controls. However, only in April 1992 were these concentrations of the same magnitude as those found in temperate studies. The average flux of particulate material under the cages, 20–49 g m−2 per day, was up to 22 times greater compared to controls. Carbon accumulated only in April 1994, implying rapid decomposition. This was supported by a 4–25-fold higher outward flux of ammonium and phosphate from the farm sediment but sediment O2 consumption was only 29–40% higher compared to control sites. It was concluded that intensive fish farming in the tropics can generate similar eutrophication effects that are observed in temperate regions. However, the results also indicated that a tropical lake system may be able to process local deposition of organic wastes better than a temperate one, suggesting that microbial decomposition may be a rapid and prominent process.