In urbanized estuary areas, water quality often deteriorates due to the impact of surface runoff or overflow during heavy rainfall events. Low impact development (LID) can mitigate this impact and improve water quality resilience. However, there were few studies on quantifying this effect of LID, particularly in estuary areas. In this study, water quality resilience is expressed as the abnormal rate of water quality during rainfall events and the time required for water quality to recover from abnormality to normal. In this study, a coupled Storm Water Management Model (SWMM) and Environmental Fluid Dynamic Code (EFDC) model is used to examine the effects of LID on runoff pollution and water quality resilience in the Shenzhen River estuary (including Shenzhen River and Deep Bay) in China. The results indicate that (1) The inflow volume into the estuary is not only affected by the drainage area but also by the service area and capacity of the sewer interception system; LID can reduce not only the stormwater runoff but also the overflow from the interception systems along rivers. (2) The marginal benefit of the LID proportion increase in pollution load reduction diminishes as the proportion of LID implementation increases. (3) LID can reduce the high value of pollution concentration caused by rainfall runoff; and the reduction effect on the rivers is greater than that on the bay. (4) The rivers and the estuary have a much higher abnormal rate than the inner bay and the outer bay; however, the estuary and the inner bay have longer recovery time than the rivers and the outer bay. The maximum abnormal rate, average abnormal rate, and recovery time of different indicators in the entire estuary area are decreased by 10%-189%, 6%-71%, and 0.8–1.1 cycles when the runoff from 80% of built-up area is treated by LID facilities; LID can significantly reduce abnormal rate of the rivers and recovery time of the inner bay. Therefore, the proposed metric and model can fully reflect the spatial variations in water quality resilience, and LID can enhance the water quality resilience of the urbanized estuary areas under rainfall.