Large-scale river rehabilitation can be a critical strategy for improving flood control and management. This paper presents our analysis of the effects on flooding of the initial phase of the river restoration program for the Pasig River System in urban Metro Manila, Philippines. The Pasig River, a 26-km tidal estuary, was once a center of commerce and political activity in Manila. It is now considered ecologically dead; sediments and large volumes of garbage impede water flow, resulting in frequent flooding in surrounding areas. The national government has initiated a program to restore the river system to its former pristine condition in the 1950s and has completed restoration of the Estero de Paco, a tributary located near the river mouth. Our current study focuses on the effects of this completed work, with particular emphasis on sediment flow and flood control. We developed and implemented a hydraulic model of the Estero in HEC-RAS to examine the extent to which localized flooding has been reduced as a result of the restoration efforts. Collected field data, supplemented by literature data, were used to support model calibration and analysis. Our simulation results show a significant reduction in the extent of flooding in the Estero, however, there is a need to address solid waste disposal and sedimentation from upstream tributaries and surface run-off to control flooding over the long-term. Further analysis is required to examine the long-term effects of in-stream vegetation on channel hydraulics, water quality, and flooding frequencies before similar restoration efforts are replicated in other tributaries.