The effects of adding an aquaculture pond to existing farming operations on nutrient use efficiency and productivity were explored. Ponds can be used to cycle nutrients from agricultural by-products such as manures and composted grasses. The production from ponds using agricultural by-products was similar to that of ponds receiving formulated pellets. The largest fraction of the nutrients fed to ponds accumulated in the sediment. Pond sediments were rich in nitrogen and potassium, but only contained small amounts of soluble reactive phosphorous. Pond sediments supplemented with phosphorous produced a similar corn yield to standard inorganically fertilised plots. Starting from a database on nitrogen flows through Kenyan highland farms, a typical farm operation was defined for each agro-ecological zpne. In the agro-ecological zones where annual temperature ranges allowed for the culture of tilapias, a tilapia pond receiving nutrients from on-farm by-products was integrated into the farming operations. Results showed that the nutrient depletion, typical for highland cultures in Kenya, is reduced, while more nutrients end up in harvestable products than in situations without aquaculture. The results are promising, but more work is needed on fine-tuning capital and labour availability for integrated aquaculture-agriculture systems to the needs or opportunities of farming households.