Macrobenthos are a key ecosystem indicator and are sensitive to changes in sediments. This study evaluated the ecological status of the Musa estuary located in the northwestern part of the Persian Gulf (Iran) by analyzing macrobenthic community structure and applying biotic indices. The sediment and water samples were collected from six creeks during the summer and winter of 2024 using a Peterson grab and Nansen bottle, respectively. The sediment grain size, total organic matter (TOM), and macrobenthic composition were analyzed. Concurrently, bottom-water physicochemical parameters, including salinity, temperature, pH, and dissolved oxygen concentrations, were measured to assess their potential influence on benthic habitat characteristics. The ecological indices, including AZTI's Marine Biotic Index (AMBI), Benthic Opportunistic Polychaetes Amphipods Index (BOPA), Shannon, Margalef, Pielou, and Simpson, were calculated to evaluate ecological quality. Seventy taxa from seven phyla were identified, with Annelida dominating (69.62%), notably Melinna sp. and Capitella sp. Jafari Creek exhibited the highest macrobenthic density in summer, while Odeleh Creek peaked in winter. Jafari Creek also showed the highest Shannon and Margalef diversity indices across seasons. AMBI and BOPA indicated predominantly unpolluted to slightly polluted conditions, except Ghazaleh Creek, which displayed moderate to severe pollution in winter. TOM positively correlated with the benthic abundance and diversity. Findings suggest that Musa estuary’s ecological status is influenced by natural dynamics and anthropogenic pressures. The study underscores the importance of integrating multiple indices for robust ecosystem assessment.