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Agrochemicals contaminate water bodies in agroecosystems, which affects the health of fishes. We assessed erythrocytic nuclear abnormalities (ENA) in Cyprinus carpio reared in uncontaminated and contaminated water bodies. We recorded micronucleus, notched nucleus, lobed nucleus, kidney bean-shaped nucleus, bi-nucleated, blebbed nucleus, karyopyknosis, nuclear shift, ooze out nucleus, and elongated nucleus at higher incidences in fish reared in the contaminated site. We observed a high percent incidence of ENA and micronucleus in fish from the contaminated site. The analysis of heavy metals with atomic absorption spectroscopy revealed that all heavy metals (Mn, Zn, Ni, Pb, Cd, Fe) were high in the contaminated site except for Cu in water and Cu and Cr in sediments. Correlation matrix analysis showed that total ENA increased with Cu (r = 0.996, p < 0.0001), Mn (r = 0.942, p < 0.0001), Zn (r = 0.517, p = 0.07), and Cr (r = 0.997, p = 0.0001). Compared to the uncontaminated site, the incidence of micronuclei was 20 times higher in the fish from the contaminated site, and this was influenced by the Cu, Mn, Zn, and Cr contents in the sediments. This study indicated that the heavy metal contamination of a water body located in an agroecosystem contributed to nuclear abnormalities in C. carpio.