Water quality parameters and plankton were analysed in two fishing harbors (Chinnamuttom and Colachel), waters along the complex aquatic ecosystem at Kanyakumari district during July 2021 - June 2022. Seasonal variations of physico-chemical parameters such as AT (27-34oC), SST (24.3-31oC), pH (7.46 -8.12), salinity (28.0-33.5 psu) ,DO (3.4-5.6 mg/l) and the inorganic nutrients such as NO3 (0.042-0.14 mg/l), NO2 (0.074-0.088 mg/l), PO4 (0.078-0.193 mg/l), SiO4 (0.480-0.797 mg/l) and NH3 (0.054-0.127 mg/l) were estimated in selected study site i.e. harbor waters. A total of 74 species of phytoplankton was recorded in Chinnamuttom harbor water and 59 species were recorded in Colachel harbor water during the study period. Bacilariophycea were dominantly recorded in both ststions.Totally 56 species of zooplankton were observed in Chinnamuttom harbor whereas 46 species were found in colachel harbour. Calanoid groups were dominantly recorded in both stations during the study period. Also the physicochemical parameters influence was correlated.Statistical tools PRIMER (Ver. 6.1.11) and Origin Pro 8.0. were employed to find the species diversity, richness and evenness were calculated.