Coastal ecosystems are increasingly threatened by human activities, necessitating effective monitoring tools to assess their ecological health. This research examines the ecological conditions of three estuaries along the Persian Gulf and Gulf of Oman, focusing on the impacts of human activities over a one-year period by utilizing macrofauna as biological indicators. Samples of macrofauna and sediment were collected from nine distinct sites, reflecting a range of contamination levels from industrial wastewater and shrimp farming to relatively unaffected areas. A total of 165 macrobenthic taxa were identified across seven groups: Annelida and Mollusca each had 65 taxa, Arthropoda had 28, Echinodermata had 3, Hydrozoa had 2, and both Nemertea and Nematoda had 1 each. The most common group was Polychaeta, accounting for 37.57 % of the total, followed by Gastropoda at 22.42 %. The ecological condition and sediment quality were assessed using biotic and heavy metal indices, specifically the AMBI and the potential ecological risk index (PERI). The analysis revealed that industrial sewage and effluents from shrimp farming are significant pollution contributors in the Khamir and Tiyab estuaries, respectively, leading to notable declines in biodiversity indices (P ≤ 0.05). The AMBI index exhibited a strong negative correlation with species richness and Shannon and Margalef indices, while positively correlating with total organic matter (TOM). Heavy metal concentrations were found to be elevated in contaminated sites, further indicating ecological stress. The results suggest that the AMBI index is a valuable tool for assessing coastal ecosystem conditions, effectively distinguishing between less affected and heavily impacted areas, and can support coastal monitoring efforts. Additionally, Capitella capitata and Clymene robusta showed resilience to pollution, while Assiminea sp. And Littorina intermedia were sensitive to environmental disturbances. These findings can inform more efficient and targeted management strategies for coastal areas, emphasizing the importance of monitoring heavy metal levels in maintaining ecological health.