The presence of heavy metals in an aquatic ecosystem can be directly linked to the incidences of mutagenicity in aquatic organisms. Thus, we appraised the presence of heavy metals in pond water samples and assessed their mutagenic potential. The water samples were collected for a period of two years for eight different seasons. Concentrations of heavy metals were analysed using microwave plasma atomic emission spectroscopy (MP-AES) and compared with the BIS and WHO standards for drinking water. Overall, the highest metal concentrations were detected during the winter season (Cu - 564.55±9.057 μg/L; Ni - 225.45±91.81 μg/L; Zn - 860±48.41 μg/L; Cr - 857.91±57.81 μg/L) followed by summer (As - 18.36±4.23 μg/L; Pb - 130.93±49.73 μg/L; Cd - 8.21±1.81 μg/L) and monsoon season (Co - 631.96±77.09 μg/L; Se - 2315.45±67.18 μg/L). The lowest metal concentrations were observed during the post-monsoon season. HPI index revealed that six sampling sites out of 11 were above the critical index of 100. In mutagenicity assays we observed that samples with a higher concentration of heavy metals exhibited higher mutagenic potential. The maximum mutagenic potential was observed during the winter and summer seasons. This study can be very helpful to policy and decision makers for water resource management and conservation strategy.