Urbanized coastal areas are well-recognized hotspots for the contaminant-enriched groundwater discharge, influencing sensitive coastal ecosystems. The present study investigates how muddy beaches in the semi-arid region alter the contaminant flux flowing into the sea using submarine groundwater discharge (SGD) estimation and hydrogeochemical analysis of coastal waters (groundwater, porewater, and seawater). Fresh SGD carries contaminants such as nutrients and trace metals in the coastal ecosystem, causing increased vulnerability towards eutrophication, harmful algal blooms, and human health. We found that SGD reaching the coast carries immense nutrient flux (155.6 mmol NO3− · day−1; 35 mmol P · day−1 and 12.4 mmol DSi · day−1) and trace metal load ranging from 0.1 to 14.9 mmol · day−1. The nutrient fluxes were higher in the upper saline plume compared to the lower plume. The muddy beach attenuates the nutrients in varying percentages of 9.7 to 22% of NO3−, 1.9 to 25.5% of P due to denitrification and phosphorus absorption, and also caused 19.6% reduction of SO42−. The reduction in SO42− leads to the formation of sulfide (HS−) that promotes the metal precipitation, resulting in the removal of Pb and Cu. This attenuation of nutrients leads to a change in the nutrient ratio (N/P = 7–11) approaching the Redfield ratio, implying the vulnerability of algal bloom at the Dehri beach. Overall, the muddy beach can serve as a natural biogeochemical reactor as it attenuates the nutrient and serves as a source for certain trace metals (Fe, Mn, Zn, and Ni), altering the composition of SGD. Probably this is the first study that emphasizes the attenuation of trace metals in the muddy beaches of a semi-arid region.