A total of 204 Cirrhinus molitorella at a stocking density of 7 individuals/m3were equally divided between three closed rectangular concrete ponds (4 m × 2 m × 1.6 m; water depth 1.2 m) with dissolved oxygen concentrations above 5.2 ± 0.3 mg/l, and pH 6.5–8.1. Water flow in the ponds was poor. The amount of feed increased from 0.81 ± 0.35 to 13.42 ± 1.89 g/fish-day throughout the experiment. Samples were collected between mid-March and October 2016, and we monitored the Cd, Cr, and Hg concentrations in gills, large intestines, small intestines, intestine contents, longitudinal muscles, and body wall, and in suspended particles and sediment in the ponds. The effect of fish growth on metal concentrations was determined. Simultaneously, the correlations between heavy metal concentrations in suspended particles, sediment, and fish body wall were assessed. The Cd, Cr, and Hg concentrations in large intestines, small intestines, and intestine contents increased over time as feed application increased, and were significantly higher in intestines than in other tissues. The Cd, Cr, and Hg concentrations in suspended particles and sediment increased significantly as time elapsed and feed increased. The Cd, Cr, and Hg concentrations in the intestinal systems increased as fish grew. Strong correlations were found between heavy metal concentrations in the intestine contents and suspended particles; intestine contents and sediment; and suspended particles and sediment, but correlations with concentrations in the body wall and other substances were weak. Positive relationships between feed provided and metal accumulation resulted from uncontrolled feeding. Poor water flow allowed unconsumed feed containing metals to supply suspended particles containing metals; these enriched the sediment and ultimately supplied metals to the fish.The results provide reference data for developing C. molitorella eco-aquaculture systems.