Pontoon bridges are preferable structures when bridges supported by piers are not economically feasible. However, bridges that are built on floating pontoons act as a barrier and can block water flow, thus affecting the transport timescales of the estuaries. The Golden Horn (GH) Estuary in the Bosporus in Turkey suffers from poor circulation conditions and is susceptible to water quality problems due to the Valide Sultan Bridge (VSB), which was built on floating pontoons in 1912, and was later relocated out of the estuary to enhance circulation. However, the Istanbul Metropolitan Municipality is currently reconsidering reinstalling the VSB in the GH, which could potentially reduce the density of traffic in Istanbul. In this study, a three-dimensional (3D) numerical model was performed to determine the best bridge alternative that would cause the minimal negative impact on the water residence time in the estuary. Toward this aim, various hydrological (high-flow and low-flow) and structural scenarios (pontoon layout and location) were developed and compared with each other. Results of the study showed that the pontoons impacted the flow fields and changed the water exchange of the estuary. In low-flow conditions, in the upper and middle estuary, pontoons caused an increase in residence time up to 30 h; however, modification in the pontoon layouts considerably benefited the renewing of the water. In addition, in the case of placing the bridge at the shallow zone, local decreases in renewal times was seen, and this alternative was found to be more applicable than the deeper alternative for the bridge location. The findings of the study also revealed the importance of analyzing residence time spatially.