This study compares nutrient and sediment retention among rice and fish farms and wetlands in valley bottoms in southern Rwanda. Small-scale wetland, rice and fishpond experimental systems were established to measure sediment, nitrogen (N) and phosphorus (P) fluxes during a 9-month period. There were significant differences in the processes contributing to sediment, N and P retention in the three systems related to system characteristics, management practices, and seasons. Overall nutrient retention was higher in the rice and fish systems, but these systems had higher inputs and outputs of sediment and nutrients. In rice plots, resuspension and discharge of sediment and nutrients to the outflow were caused by ploughing and weeding during the first 3 months of the culture period. In fishponds, nutrients and sediment discharge were associated with water renewal and sediment removal during the last 5 months of the farming period. The undisturbed wetland plots had the lowest outflows of sediment and nutrients. Nutrient uptake and accumulation in biomass was much higher in rice and wetland vegetation than in fish biomass. In fishponds and wetlands, nutrients accumulated in soil, whereas rice plots showed a decrease or depletion in nutrient storage. To increase nutrient utilization at the plot level, sediment and nutrient discharge from land preparation and rice transplanting should be reduced by better farm practices. Within a catchment, nutrient flows can be integrated by using fishpond sediments for crop farming, by incorporating natural wetlands in crop rotations or using them as buffer zones.