This study observes and interprets the spatio-temporal variation in the oxygen and hydrogen isotopic composition (δ18O, δD) of shallow groundwater in the Southwestern Coastal state of India, Kerala, in terms of seasonally varying rainfall, physiography, and hydrogeological settings of this region. This study identifies effective groundwater recharge sources and their relative contributions and provides first-order estimates of submarine groundwater discharge by interpreting the spatio-temporal variations in the stable isotopes of oxygen and hydrogen in groundwater, collected from 225 locations for pre-monsoon and post-monsoon seasons in conjunction with the isotopic composition of rainfall. Spatio-temporal variations in the δ18O and d-excess, with other hydrogeological data, reveals that: (1) ∼4.9 Billion Cubic Meter (BCM) of fresh water from rainfall during May to October mixes with ∼5.9 BCM of residual pre-monsoon groundwater across Kerala. (2) ∼ 11% area of Kerala is additionally recharged by the NE monsoon rainfall. (3) The annual groundwater recharge varies physiographically from ∼2.2 BCM in the lowland to ∼1.5 BCM in the midland and ∼1.2 BCM in highland regions. (4) On an annual basis, 41% of replenishable groundwater is drained as SGD into the Arabian Sea.