High concentration of cadmium and lead are hazardous to environment. The study isolated and identified potential fungal, bacterial and hyperaccumulating plants as bioremediators in contaminated rice ecosystem. Fungi were identified morphologically and with the use of internal transcribed spacer (ITS) region sequencing. Bacteria were identified using 16S ribosomal RNA sequences. Plants were analyzed for Cadmium and Lead accumulation in root and shoot tissues using atomic absorption spectrophotometer (AAS). Fungal species including Penicillium janthinellum, Trichoderma hamatum, Trichoderma harzianum, and Curvularia lunata along with bacterial species such as Bacillus cereus, Bacillus thuringiensis, Pseudomonas gessardii, Lysinibacillus xylanilyticus, Lysinibacillus sphaericus, and two species of unidentified bacteria were identified. Plants predominant in the area includes Cyperus difformis, Scirpus juncoides, Fimbristylis miliacea, Centella asiatica, Sphagneticola trilobata, and Monochoria vaginalis. Cadmium was detected in the shoots of S. trilobata (3.2 mg kg−1) and roots of C. asiatica (3.6 mg kg−1). Lead was found in the shoots of C. asiatica (2.8 mg kg−1) and roots of both S. juncoides (15.00 mg kg−1) and F. miliacea (15.00 mg kg−1). Phytoremediation potential of S. juncoides, F. miliacea, C. asiatica and S. trilobata was observed. Heavy metal resistant microbes can be harnessed as a very useful biological tool for in-situ bioremediation.