Animal-source foods (ASF), such as fish, provide a critical source of nutrients for dietary quality and optimal growth of children. In sub-Saharan Africa, children often consume monotonous cereal-based diets, a key determinate of malnutrition such as stunting. Identifying existing sources of ASF for children’s diets will inform the development of nutritious food systems for vulnerable groups. Here we adopt a food systems framework (sensu HLPE, 2017) to examine links between aquatic- and terrestrial-based ASF sources with ASF consumption and dietary diversity in rural children aged 6-23 months in sub-Saharan Africa. Employing a novel approach, we merged existing geo-tagged nationally-representative datasets, including Demographic and Health Surveys for Malawi (2015-16, n=3995) and Zambia (2013-14, n=2333) with spatial data on proximity to inland fisheries (waterbodies ≥0.1km2) and formal markets. We found that children living closer to inland fisheries were more likely to consume fish and aquatic-based ASF, and exhibit higher dietary diversity. Children did not always consume more ASF if they lived were closer to a formal market or in a house that owned livestock. We found that inland fisheries are one of the most important sources of ASF for rural children in sub-Saharan Africa. We also demonstrate that secondary datasets provide a useful methodology for understanding the role of food systems for diets. As food systems transition, it is important that policy and programs preserve components of the existing food system – namely inland fisheries - to ensure the ongoing provision of nutrient-dense fish and aquatic-based ASF for the dietary quality of infants and young children.