Low-relief coastal cities have experienced increased flooding due to climate change. During high tides or swell surges, stormwater canals or pipes can be inundated by coastal waters, causing suspended solids (SS) to accumulate at the conduits’ outfall. The City of Valparaiso (Chile) is currently upgrading its stormwater network with costly underground stormwater aqueducts such as the coastal “Argentina stormwater underground canal” (ASC). However, soon after the ASC was put in operation, sea water intrusion and bidirectional flow at the lowest sectors of the canal decreased its water conveying capacity, and SS (that otherwise would have been carried to Valparaiso Bay) accumulated in the lower sectors of the canal, close to its outfall. Urban growth and reduction of pervious land covers could worsen the current situation. Therefore, the current ASC outfall seems to be an unsustainable solution to conveyance of rainwater and SS. In this research, a hydrodynamic model of Valparaiso Bay and the ASC is presented. The current ASC hydrodynamic regime is described. The validated hydrodynamic model is used to explore the feasibility of using a submarine outfall to transport the accumulated muddy water to an offshore location. The effects of sea level rise on the existing stormwater canal are studied, and its potential to further prevent an efficient conveyance of rainwater from the city to Valparaiso Bay is explored.