The reuse of effluent waters and sediments from African catfish (Clarias gariepinus) recirculation aquaculture systems requires a deeper understanding of the nutrient and energy flows and material pathways. Three semi-commercial systems, differing in stocking density, were sampled for nutritive and pollutant elements of the input-(tap water, feed) and output pathways (fillet, carcass, process water, sediments) by ICP-OES/MS and calorimetry. Highly water-soluble elements, e.g., potassium, accumulated in the water, whereas iron, copper, chromium and uranium where found in the solids. Feed derived phosphorous was accounted for, 58.3-64.2% inside the fish, 9.7-19.3% in sediments, and small amounts 9.6-15.5% in the process waters. A total of 7.1-9.9% of the feed accumulated as dry matter in the sediments, comprising 5.5-8.7% total organic carbon and 3.7-5.2% nitrogen. A total of 44.5-47.1% of the feed energy was found in the fish and 5.7-7.7% in the sediments. For reuse of water and nutrients in hydroponics, the macro-nutrients potassium, nitrate, phosphorus and the micro-nutrient iron were deficient when compared with generalized recommendations for plant nutrition. Low energy contents and C/N-ratio restrict the solely use of African catfish solids for biogas production or vermiculture. Using the outputs both for biogas supplement and general fertilizer in aquaponics farming (s.l.) (combined with additional nutrients) appears possible.