The estuary receives varying levels of anthropogenic inputs that significantly influence the benthic biota and suppress ecological health. Thus, multiple parameters (natural and anthropogenic) and meiofaunal community structure was assessed in the Patalganga estuary surrounded by industrial area. The eastuary have been divied in three distinct zones based on salinity gradients for assessment. In total. 16 meiofaunal taxa were identified with free-living Nematoda being the most dominant. Notably, low meiofaunal richness and density were observed in the upper and lower parts of the estuary (zones Z3 and Z1) during the pre-monsoon season, indicating different levels of envirmental perturbation. Zone Z1 was characterized by high hydrodynamic properties and significant human physical activities, while Zone Z3 showed high levels of pollutants. Principal Component Analysis (PCA) revealed a clear distinction, with higher levels of pollutant chemical elements (PCEs) recorded in Z3. Additionally, n-MDS ordinations based on meiofaunal abundance indicated differentiation with partial overlap, suggesting significant impacts in Z3 and Z1, supported by low Ne/Co ratio values. BIOENV results indicated that environmental parameters (suspended solids, sand, organic carbon) and PCEs (Hg, Cr) are influencing the meiofaunal community at a higher taxonomic level, leading to poor ecological status. Therefore, the low resolution of meiofaunal taxa can be reliably used to assess the impairment of estuaries. This study underscores the importance of monitoring anthropogenic impacts on estuarine environments to ensure their health and sustainability.