Marine causeways are becoming more common in many coastal regions to improve vehicular transportation and social integration across landscapes segmented by bays and estuaries. The construction of barrier-type structures has profound implications by altering the geomorphological, hydrodynamic, and ecological conditions in the coastal marine environment. This study investigates the impact of one such newly constructed marine causeway in an enclosed bay in the Arabian Gulf. We hypothesized that the underwater structure of the bridge affects hydrodynamic and physicochemical conditions in the bay. Through extensive physicochemical monitoring, we found that the bridge acted as a physical barrier diminishing tidal currents, thereby resulting in decreased water exchange and heightened stagnation within the bay. Consequently, environmental gradients intensified and nutrient dynamics altered across the bridge. This will have implications for the plankton dynamics, ecosystem function, and overall health of the bay and its surrounding waters. Based on these results, it is recommended to increase efforts to mitigate the stagnation in the bay. Additionally, future coastal development needs to avoid further compromising the water exchange ability of the bay. Our findings also highlight the importance of continuous monitoring and adaptive management strategies to mitigate the environmental impacts of such developments.