The use of purified slaughterhouse wastewater in carp ponds, and the use of wastewater from the pond for the irrigation of agricultural fields, was the basis for the construction of an integrated system of agricultural production as a sustainable solution for the food and fish production industries. The negative side of such integrated production systems is the concern related to the safety of fish meat produced in such a system. The aim of this research was to determine the concentration of heavy metals and metalloids in the wastewater from the slaughterhouse, in the pond water and sediment, in the carp tissue and in the water leaving the pond, and to evaluate the effectiveness of the integrated system and the safety of the produced fish. Sampling was carried out in spring and autumn. The mean concentrations in all water samples (µg/L) were: As (12–125), Cd (0.12–4.2), Hg (1.14–14.21), Pb (<0.1–17.2), Cu (<0.1–44.6), Fe (17.02–425.2) and Zn (2.91–186.2), with the highest numbers in the wastewater, where it was above the prescribed limit values for the wastewater discharged from the slaughterhouses into natural recipients in both samplings. The efficiency of the wastewater treatment plant for heavy metals and metalloids was very high, in the range of 87% to 98%. The water from the pond corresponded to class 3 in terms of the concentration of heavy metals and metalloids both in spring and autumn, and can be used freely for breeding cyprinid fish species. The water from the irrigation canal corresponded to class 2/3 and can be used for irrigation. The mean concentrations of heavy metals and metalloids in the sediments (mg/kg) were: As (3.00–4.88), Cd (0.16–0.96), Hg (0.21–1.47), Pb (0.77–2.29), Cu (49.60–60.90), Fe (3.94–5.32) and Zn (92.8–115.20). The content of heavy metals in different organs of carp differed significantly depending on the season. The trend of heavy metal accumulation in common carp muscles in spring was: Zn > Fe > Cu > Pb > Hg > Cd > As, and in autumn: Zn > Fe > Cu > Pb > As > Cd > Hg. Metal concentrations in the examined fish samples were far below the WHO guidelines. It can be concluded that carp produced in a pond supplied with purified wastewater from the slaughterhouse industry, in terms of the concentration of residues of the tested heavy metals and metalloids, is safe for human consumption.