The submarine groundwater discharge (SGD) into the sea is known to alter various biotic and abiotic properties of coastal waters. However, its influence on the lower trophic levels, namely, meiofauna, is poorly understood. This study highlights the impact of SGD on the density, distribution, and diversity of intertidal meiofaunal communities along the subterranean estuaries (STEs) of the southwest coast of India (Arabian Sea). As an outcome of extensive field sampling between 2019 and 2022, we found that groundwater discharge has a direct influence on the local meiofaunal communities. Significant decline in meiofaunal density and diversity in the SGD impacted sites with 2 to 4 times lower densities than the unimpacted sites were documented. Lower groundwater salinity, lesser organic carbon content, hypoxic sediment conditions, and lower mean grain size in STEs can be the major driving factors determining the lower meiofaunal densities. δ