A bio-resource flow analysis using participatory resource mapping was conducted in Chingale Area, west of Zomba District in southern Malawi. The analysis was aimed at providing the basis for designing an integrated agriculture-aquaculture system that would optimize utilization of on-farm resources for a cost effective aquaculture production system. Results showed that Chingale has over 18 crop species and five animal species that have potential for integration into the farming system. However, only 33% of the sampled farmers were integrating over 5 species (both crop and animal species) in agriculture systems resulting in low economic efficiency, low incomes to the farmers and low sustainability of farming systems. The availability of fertile land, water, and species, if properly designed, can reduce input costs thereby increase production which would result in sustainable higher incomes for the farmers.