Terrestrial inputs, such as submarine groundwater discharge (SGD) and river discharge, modulate primary production in coastal estuaries, but exposing their independent roles remains challenging. This study examined the interactive role of nutrient flux and tidal variability on primary productivity along the Nizampatnam coast (Andhra Pradesh, India) during the pre-monsoon seasons of 2024 and 2025 by the application of 222Rn isotope and nutrients like nitrate, nitrite and orthophosphate along with the chlorophyll-a as a productivity as an indicator across two different pre-monsoon seasons in relation with tidal variations. Seawater, groundwater, porewater and river water showed that mid-tide conditions yielded most productivity, attributed to both nutrient discharge and the favourable hydrodynamic conditions. During high tide, the nutrient inputs from SGD were enhanced, but the increase in salinity and temperature suppressed primary productivity. Maximum SGD driven nutrient fluxes were estimated to be 1.95 × 1012 μmol/m/d (Nitrate- NO3−), 7.15 × 1011 μmol/m/d (Nitrite- NO2−), and 8.24 × 1011 μmol/m/d (ortho-phosphate-PO43-). Besides, uranium has been found in groundwater exceeding WHO limit within the range of 30–60 μg/L. Nutrients and productivity showed positive correlation across all tidal dynamics (PO43− r = −0.67, p = 0.07; NO3− + NO2−=NOx r = −0.36, p > 0.05) indicating nutrient accumulation under low biological uptake conditions. The study highlights how SGD and nutrient flux reinforce productivity interannually with tidal dynamics in the Tropical Indian coast.