The present study encompasses an assessment of annual and long term variations in groundwater level of Peruvanthanam and Valiyathodu sub-watersheds and its correlation with rainfall occurrence. The seasonal variations in phreatic surfaces of both sub-watersheds reveal that unlike Peruvanthanam, Valiyathodu sub-watershed shows maximum fluctuations in groundwater level during post monsoon season. Average rainfall in Peruvanthanam sub-watershed during this period was 3832.28 mm and the average water levels in the observation wells CGWBp1 and CGWBp2 were 4.86m and 2.62m respectively. In 2007 when there was an increase of 1199.72 mm rainfall from the average. Well no. CGWBp1 shows a decrease in water level from 4.36 to 4.10m ie, 0.76 m (15.64%). The corresponding decrease in value observed in groundwater level of well no CGWBp2 was from 2.62m to 2.20m ie, 16.03%. When both the well data are compared, greater variations are observed, in well no.CGWBp2 during increase in rainfall. This is a reflection of the greater porosity and permeability of the ground material in an around the well. Similarly in 2000, there was a decrease of 1296.78mm in rainfall from the average. In well no CGWBp1 there was an increase in depth from 4.86m to 5.59m ie, 0.71m (14.61%). The corresponding value for well no CGWBp2 was from the average value of 2.62m to 2.95m ie, 0.33m (12.60%). Average rainfall of Valiyathodu sub-watershed was 4099.82mm and the average water level in CGWBv1 and CGWBv2 are 9.12m and 5.64m respectively. In 2005 when there was an increase of 1031.68mm rainfall from the average well no. CGWBv1 shows a decrease in value from 9.12 to 7.82 (14.25%). The corresponding variations observed in well no. CGWBv2 was from 5.64m to 5.16m (8.51%). In 2002 there was a decrease in rainfall to 3089.00mm from the average value of 4099.82mm. The variation in groundwater level observed in well no. CGWBv1 in accordance with this is from 9.12m to 10.01m ie, 0.89m (9.76%). The corresponding variations observed in well no. CGWBv2 is from 5.64m to 5.98m ie, 0.34m (6.03%). When both well data are compared, greater variations are observed in well no CGWBv1 during both increase and decrease in rainfall. This shows that sub surface phreatic aquifer material in around well no. CGWBv1 has more permeability compared to CGWBv2.