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Hydraulic structures such as darns, locks or diversion gates, in the upstream or tributary of an estuary system can control necessary freshwater discharge to meet downstream water quality standards. One of the most significant purposes of these structures is maintaining target salinity to satisfy the environment concerns, such as fishery spawning in the high-flow season and drinking water criteria in the low-flow period. In order to evaluate possible alternative regulations for the reservoir operation, a reliable three-dimensional (3-D) hydrodynamic model is required as a management tool to simulate the impact of salinity variations due to release policy changes. This paper discusses the 3-D capability of presenting a complicated riverine- estuarine process for the release policy of Conowingo Reservoir, Susquehanna River, near the head of Chesapeake Bay, from an extremely dynamic system (Upper Chesapeake Bay-C&D Canal-Delaware Bay), as shown in Figure 1.