Global warming and the subsequent events of climate change and variability may have even greater repercussions for marine ecosystems than for terrestrial ecosystems, because temperature influences, water column stability, nutrient enrichment, and changes in the biodiversity of plankton communities and its reproductive cycles. Any change in the plankton diversity and abundance would affect the marine food-web and other trophic levels. In order to understand the impacts of climate change and its variability on the tropical coastal and marine ecosystems, study has been undertaken to investigate the diversity and trophic structure of plankton in the most important tropical estuarine system, a unique coastal marine environment in South India, as it is connected with mangrove ecosystem, brackish water and Bay of Bengal. The long term continuous monitoring survey showed (20 years of intensive study from 1988 to 2008) remarkable variations in environmental parameters, chlorophyll a concentrations and diversity of species, abundance of phytoplankton and zooplankton communities. Besides, it showed seasonal variations also: - being highest in summer (April – June) and lowest during monsoon (October – December). There were wide temperature fluctuations (range: 22.5 – 33.8 oC), salinity gradients (2.9 – 34.5PSU) and chlorophyll a concentrations (1.4 – 18.6 µg l-l). The overall mean abundance of phytoplankton 4.3 fold and zooplankton 3.6 fold were higher in summer than during monsoon. The low diversity and abundance of plankton (both phyto and zooplankton) during monsoon might be due to un-favorable climatological conditions (low temperature and low salinity), disappearance of many species, abundance versus, scarcity of food and high turbidity conditions in the water column. The series of data collected on plankton diversity and abundance over the past 20 years showed interesting observations and these have included changes in species distribution and abundance, the occurrence of neritic/oceanic in estuarine ecosystems and community shifts. Thus, climate change and its variability exert major influence on the diversity of plankton communities and significantly affect the marine food webs and other trophic levels.