Wetlands play an important role in the livelihoods of many rural households particularly in sub-Saharan Africa. However, due to decline in rainfed terrestrial agriculture, many wetlands are being encroached upon to grow crops. The question to any wetland scientist/policy maker in the region is: what efforts can be made to achieve a balance between human needs for food and income and maintenance of ecosystem integrity?.This study analyses the potential of smallholder integrated aquaculture farming systems (called “Fingerponds”) around the Lake Victoria wetlands in Kenya. Various analytical tools were used to evaluate the biophysical suitability, nutrient flows, benefits and environmental implications of this innovative technology. The critical biophysical factors determining Fingerponds productivity are site selection and water supply. The analysis of nutrient flows in the entire agroecosystem using nitrogen as the currency indicated that the total system throughput, and hence the overall productivity of the system were low. Fingerponds contributed to household livelihoods by providing protein and income and added diversity to the household activities with minimal impacts on the natural environment. With careful implementation and adaptive management, Fingerponds can be incorporated into national wetland policies and enhance the balance between economic development and environmental conservation.