The purpose of this study was to determine the effects of frequent species population fluctuations and the impact of different rates of exploitation on other ecological links in the food web. The mass‐balanced Ecopath model represents the trophic interactions among the 31 defined functional groups in the Kolahi to Dargahan area, with five main species, including Trichiurus lepturus , Saurida tumbil , Nemipterus japonicus , Sillago sihama , and Cynoglossus arel (from April 2018 to April 2019). To investigate the effects of fishing and environmental disturbances, the Ecopath modeling approach combines software for analyzing ecosystem trophic‐level balances with population dynamic models. In the past 5 years, Hormozgan province has caught more than 45% of the benthic fish caught off the northern coasts of the Persian Gulf. From Kolahi to Dargahan, one of the most important fishing grounds in this province's southeast is located. Food web models are used to represent a marine system's current state, assess stock levels, and predict change over time. Over a year, the first five dominant fish in the study area, S. tumbil , S. sihama , C. arel , N. japonicus , and T. lepturus , were biometrically measured, and their population dynamics parameters as well as feeding ecology indices were analyzed. According to the trophic‐level index results, the five most common species studied in this study belonged to the third ( N. Japonicas , S. sihama , and C. arel ) and fourth ( T. lepturus , and S. tumbil ) trophic levels. The key species with the greatest impact on other groups of studied species were identified as S. tumbil and T. lepturus , respectively. The estimated ecosystem indicators were the system operational power (75846.797), the primary production/respiration ratio (0.034), the connectance index (0.159), and the system omnivory index (0.253). A pedigree index (PI) of 0.38 was estimated for the present model. Overexploitation of T. lepturus could disrupt the aquatic food web and adversely affect the long‐term sustainable use of aquatic resources, according to data. As a result, ecosystem‐based fisheries management should be implemented to find a more appropriate solution to sustainable exploitation in the studied habitat, an important fishing area in the Persian Gulf's north.