The present study aims to assess the physicochemical parameters and distribution of aquatic macrophytes of seasonal wetlands flowing into the coast of Palk Bay, southeast coast of India. We tested the hypothesis whether there is any statistically significant difference in physicochemical parameters and macrophyte communities among study location. Water quality parameters such as temperature, pH, salinity, TDS, DO, turbidity and electrical conductivity, and the aquatic macrophyte diversity were estimated in all three stations. One-way analysis of variance (ANOVA) and Pearson correlation were employed to assess the relationship between water quality parameters, and the water quality index (WQI) was computed to assess the status of water conditions. The ANOVA revealed that there is no statistically significant difference (p > 0.05) in water quality parameters among the three stations. The lowest f value 0.180 was recorded for pH and highest of 2.478 for TDS. A total of 7 submerged macrophytes, namely Ceratophyllum demersum L., Egeria densa Planch., Lemna minor L., Marsilea quadrifolia L., Sagittaria guayanensis and Isoetes riparia; 6 rooted floating weeds, namely Potamogeton nodosus Poir., Nymphaea odorata Aiton., Nelumbo nucifera Gaertn., Myriophyllum spicatum L. and Hydrilla verticillata; 1 floating, namely Eichhornia crassipes Kunth; and 1 rooted macrophyte, namely Najas minor, were recorded in Tharavai wetland. A deplorable water quality condition was found in the selected study area, which was evidenced from WQI (> 76%). Of this, submerged aquatic vegetation is used as the water quality key indicator, and it exists where there is a better water quality condition. The EC, TDS and turbidity negatively influenced the aquatic macrophytes. Therefore, there is a need for some adaptation measure to maintain the water quality for more extended period for domestic use.