Saltwater intrusion is detrimental to water utilization. It is of vital significance to study the joint impact of runoff and tide on salinity and the risk of saltwater intrusion. To analyze the risk of saltwater intrusion, this paper proposes two concepts: critical runoff–tide level line and guarantee rate of freshwater. Taking Nandu River Estuary in China as a study case, a three-dimensional (3-D) hydrodynamic and salinity numerical model is built. Critical runoff–tide level lines are obtained to determine the occurrence of saltwater intrusion. To quantify the guarantee rates of freshwater, copula joint distribution is utilized, which connects the numerical model and daily hydrological characteristics. Guarantee rates of freshwater are obtained under different amounts of water intake (0, 10 m3/s, 20 m3/s, 30 m3/s). In addition, critical locations of water intake that satisfy different guarantee rates (80%, 85%, 90%, 95%, 99%) are identified. All the results will provide technical support for risk evaluation of saltwater intrusion and decisions on water intake location.