Many power plants require large quantities of water for cooling purposes. The water taken from the source water body (e.g., lakes, estuaries, bays and rivers) circulates through the plant and returns to the source through outfall with a higher temperature. For optimal performance of the power plant, the intake inlet and discharge outlet should be meticulously placed so that the heated water will not recirculate back into the power plant. In this study, the Flow module of the Delft3D software is employed to simulate the temperature transport within the study area in three-dimensional and nested format. Model results are used to optimize the location of intake inlets, outfall outlets and diffuser port orientations. The physical processes used in the study are tidal fluctuations, winds, river discharges, salinity and temperature. The subject power plant (power plant parameters presented in this paper are realistic; however, they do not target any specific power plant within the study area) has a nominal capacity of 2600 MW and is planned to be located in Delaware Bay, USA. Existing field measurements are used to calibrate the model in a coupled two-staged fashion for main tidal constituents, currents and water temperature. The sensitivity of the model against various input parameters is tested, and conservative values are selected. The location of the intake is fixed, and the location of the outfall is changed until the thermal impact to the intake is less than 1 • C. Analysis of the results shows that there is a linear logarithmic relation between the excess temperatures at the intake inlet and horizontal eddy diffusivity. The k − turbulence closure results in higher excess temperature and a more conservative design. Extending the outfall location to the deeper portion of the estuary combined with port orientations reduces the impact by keeping the thermal plume away from the intake inlet and meeting the established criteria. It is concluded that an approximate distance of 1300 m is the optimal location for the power plant outfall outlets. In addition, the diffuser ports should not discharge the heated water toward the intake and have to be oriented away from the line connecting outfall to the intake.