Regional climatic changes reflect the microclimatic variations and these affect the water resources of a region. Urbanization and population growth significantly influence microclimates, impacting groundwater resources and Land Surface Temperature (LST). The climatic variables (rainfall and temperature) interplay with geospatial parameters such as Land Use Land Cover (LULC), LST influence the quality and quantity of groundwater. Hence, this current approach employs geospatial techniques to explore the interrelationship between these variables by studying the long-term variation for a period of 20 years (1997–2018) to assess the microclimate variation and its impact on groundwater resources of a coastal aquifers with complex lithology. Results reveal a notable increase in minimum and maximum temperatures, with an average annual rise of 0.5°C predominantly along the western part. Spatial rainfall variation for the study period was higher in the northern region influenced by urban heat islands. The change in LULC reflected a 12% increase in agricultural areas and a 1.7% expansion in habitation, accompanied by a decline in surface water bodies in 2018. Maximum increase in electrical conductivity(EC) is observed along the southern coastal region, indicating rise in ionic concentration due contamination from sea water, urban and agricultural sources, witnessed by the isotopic signatures. Comparison of the depth to groundwater between the different study periods indicate a maximum depletion of 49m in northeastern and western regions due to extraction for domestic water supply, agriculture and mining. Further, a maximum rise of 14m in the regions adjacent to the reservoirs was observed, during 2018. The current study reveals the relationship between microclimate and groundwater (quality and the quantity) is predominantly observed in the northern and western parts of the study area. Our findings suggest that managing groundwater extraction and improving land use practices are essential for sustainable development, primarily through policy and governance.