The investigation of the absence of the Babolsar fishing port breakwater on the sedimentation regime and hydrodynamic behavior of the Babolrud River estuary, particularly under summer low-flow conditions, is crucial. During summer, the upstream rubber dam is closed to supply agricultural water, reducing river inflow and increasing sediment intrusion from the sea. A scenario simulating breakwater removal was defined for the first six months of 2023 to examine sediment deposition in the study area. By collecting wind, wave, and topographic data and performing large-scale Caspian Sea modeling with MIKE21, wave and current fields were extracted and used as inputs for a small-scale hydrodynamic and sediment transport model at the estuary. The small-scale model, executed with detailed mesh and EchoMap data, simulated only the breakwater removal scenario. Results indicate that removing the breakwater increases wave penetration, promotes alongshore currents, and induces vortices at the estuary mouth, creating favorable conditions for sediment accumulation. Within the river and in front of fishing docks, changes in velocity vectors, formation of local eddies, and fine-grained sediment deposition are possible. These findings demonstrate that fishing port breakwaters are critical in reducing wave penetration, controlling coastal sediment intrusion, and maintaining estuary hydrodynamic stability. Their removal, particularly under summer low-flow conditions caused by the rubber dam closure, leads to significant sedimentation and a continuous need for dredging.