Strong conservational management needs comprehensive data on the status of biodiversity. However, effective methods to document aquatic biodiversity are either lacking or less in use. Environmental DNA (eDNA), often released by the organisms into the environment (e.g. water, soil) offers a great opportunity for examining the biota in aquatic ecosystems. Here, we have conducted a metagenomics study on eDNA sample collected from Muttukadu, Tamil Nadu, India to portray the biodiversity in a backwaters featured environment. Shotgun metagenomic approach with Illumina® NextSeq 500 sequencing yielded 88.4 million raw reads. The processed clean data were assigned as 80% prokaryotes, 0.4% eukaryotes, ̴ 2 % viruses and ~ 17 % remain as unknown or un-identified. Using this approach, we detected 112 families across the major phyla of eukaryotes. The approach has the potential to discover small micro-eukaryote, unseen species and, our data represents major phyla from both estuarine and marine environments.  This includes phyla that are of conservational significance and ecologically sensitive. Given the sensitivity, efficacy, and the cost-effectiveness of the method, we suggest this tool for an introductory understanding of biodiversity structure in a backwater environment during biomonitoring assessments.