The present study is an attempt to investigate the impact of coastal morphology on the distribution of heavy metals in the bottom waters of the Pennar Coast, southeast coast of India. A total of 20 bottom water samples (~ 1 m) were collected using shallow water sampler. The falling sequence of heavy metals is Fe > Mn > Pb > Co > Zn > Ni > Cr > Cu > Cd > As and Fe > Mn > Pb > Co > Ni > Cr > Zn > Cu > As > Cd during pre- and post-monsoon, respectively. Fe was the dominant and the Cd and As were the lowest concentrated metals during both seasons. The mean concentration of metals except Cr and As was high during the pre-monsoon. Overall, concentrations of heavy metals were relatively low and mostly within USEPA limits. The concentration of metals shows decreasing trend while moving toward confluence point in both the seasons. The obtained data set was assessed to various statistical analyses such as factor analysis and cluster analysis. Factor analysis yielded three different factors loading with distinct variance while cluster analysis accounted for two clusters in both the seasons. Further, multi-temporal satellite images (Landsat 8) were extracted to monitor the shoreline changes. After analyzing the satellite images, predominant changes were observed at the mouth opening. Specifically, lagoon mouth closure was observed during the pre-monsoon season, followed by its opening during post-monsoon. The current study clearly indicates the role of morphology; viz., seasonal lagoon mouth opening might be the major factor for significant seasonal variations among the studied heavy metals.