Understanding the effect of environment on macrobenthic invertebrate in naturally occurring repeated mesohabitats from the warm-temperate zone river

•Present study focuses on the effect of heterogeneous mesohabitat (Rapid-Pool-Benchland) on Macrobenthic Invertebrate (MBI) indices.•pSEM was applied to understand the complex relationship between meso-scale habitat structure, environment and MBI indices .•Significantly, mesohabitat width, soil moisture, pH, Total Nitrogen and Total Phosphorous was linked with changes in the MBI abundance and total number of taxa.•The three mesohabitats differ for MBI abundance, while only rapid and pool for MBI total number of taxa.