Abstract: Background and Objective: Aquaculture operations that use floating net cages have become one of the primary mean of intensive fish-culture in Lake Maninjau. The fish-culture species studied were Cyprinus carpio (C. carpio) (T1), Oreochromis niloticus (O. niloticus) (T2), Osphronemus goramy (O. goramy) (T3) and Clarias gariepinus (C. gariepinus) (T4). The objective of the research was to estimate the nitrogen (N) and phosphorus (P) loads into Lake Maninjau. Materials and Methods: The capacity of floating net cages was approximately 32 m3 (4×4×2 m) with densities of 32 fish m–3 in triplicate groups. Approximately 1,500 kg of feed was used in each cage during the experiment. The difference of N and P loads from different fish species were analyzed using one-way ANOVA (SPSS 16.0) computer software. Results: The total N loads into the water bodies from T1, T2, T3 and T4 were estimated at 37.93±2.59, 49.90±5.17, 45.90±4.18 and 20.35±4.12 kg t–1 of fish production, respectively. The P load was estimated to be 18.30±0.12, 20.01±0.99, 22.60±0.80 and 13.93±1.47 kg t–1 of fish production, respectively. Every ton of feed consumed by each fish species will contribute as much as 38.26±2.55, 35.68±1.69, 32.12± 0.39 and 48.99±2.35 kg N load into the water bodies, respectively. The P load was 11.45±2.43, 9.11±0.21, 8.34±0.04 and 12.51±0.30 kg, respectively. Conclusion: The C. gariepinus species is preferred for aquaculture operations at Lake Maninjau, because it minimizes N and P load releases into water bodies which can maintain sustainable aquaculture operations.