Coastal reservoir contributes to alleviating the freshwater shortage in stressed areas, and the salinization of reservoir water is one of the most important challenges that coastal reservoir faced. Field-investigation indicates that there are many deep pools located at reservoir bed, and a large amount of high-salinity water was found within a deep pool which was hardly be desalted. Laboratory experiments and numerical simulations with different depth and locations of deep pools were conducted to further discuss the influence of deep pool on the salinization of reservoir and adjacent aquifer. Results showed that deep pool has greatly increased the salinity of reservoir water due to high-salinity water stored in the deep pool, which may act as an extra source of saltwater to the coastal reservoir during the dry season. The increasing depth of the deep pool was found to have negative impacts on the salinity of reservoir water, and as the distance from the deep pools to dam increased, the salinization extent in coastal reservoir decreased. Salinity data from the numerical simulations in coastal reservoirs and adjacent aquifer were matched the experimental data well. Flow field indicates that there is a high exchange capacity zone occurred from the deep pool to the seaward boundary, which gave the reasonable reasons for the existence of high-salinity water within deep pools. Those findings highlight the significant influence of deep pool on the salinization of the coastal reservoir, and explain the increased salinization by the deep pool.