Heavy metal accumulation in aquaculture farms has become a major problem due to the widespread use of artificial feed to enhance fish productivity. To estimate the contamination level and identify metal sources, we investigated the amounts of seven heavy metals (Cu, Zn, Pb, Cd, Cr, Ni, and Mn) in the surface water of commercial fresh water aquaculture farms in a south Asian tropical coastal area. Atomic absorption spectrometry (AAS) was used to analyze 36 water samples from 12 commercial fish farms. The results demonstrated that the range of three heavy metals were detected in a decreasing order of Mn (0.0574–0.4100 mg.L−1) > Zn (0.0125–0.3250 mg.L−1) > Cu (0.0275–0.085 mg.L−1). In all samples, the remaining four heavy metals (Pb, Cd, Cr, and Ni) were below the detectable level (BDL). Except for Mn, the amounts of the metals examined were below WHO and USEPA guideline values. According to the findings, the levels were found to be safe for drinking, agriculture production, and aquaculture. There was no significant correlation (p > 0.05) between heavy metal concentrations and water quality parameters, indicating that pollution came from diverse sources and that no single factor was controlling their levels. Furthermore, Analysis of Variance (ANOVA) revealed no significant differences in the mean metal values among the fish farms (p > 0.05). Multivariate analyses (CA and PCA) demonstrated the association and sources of metal in the study area. Although metal levels were not beyond the threshold limit, it is recommended that suitable measures and continuous monitoring should be undertaken to reduce heavy metal pollution in aquaculture farms and prevent water quality degradation.