In aquaculture environments, organic enrichment significantly alters the chemical composition of pond sediments, leading to increased levels of organic matter, sulfur, and iron, alongside a reduction in pH. One promising approach to improve nutrient cycling and remediate contaminated sediments is the use of bioremediation through polychaetes. The selection of native species is crucial to mitigate the risks associated with introducing non-native, invasive species that may act as disease vectors or compete with native populations. This study, conducted from 2018 to 2020, aimed to identify and introduce polychaete species from the Persian Gulf with potential for bioremediation. A total of 41 sampling stations were selected across three provinces in the Iranian waters of the Persian Gulf—Hormozgan, Bushehr, and Khuzestan. Sediment samples were collected using a Van Veen grab sampler, washed with seawater, and analyzed for polychaete identification. The study identified 23 polychaete species from five families: Eunicidae (2 species), Capitellidae (3 species), Spionidae (5 species), Sabellidae (7 species), and Nereididae (6 species). The results highlight the potential of native polychaetes in bioremediation, enhancing the quality of aquatic substrates and contributing to the preservation of local ecosystems. These species play a vital role in the health and sustainability of ecosystems by degrading pollutants and improving environmental conditions. Thus, using native polychaetes for bioremediation can strengthen biodiversity and reduce the risks posed by non-native species in aquatic management and conservation.