This research describes how integration of engineering and environmental aspects into the planning with extensive use of numerical hydrodynamics models by using MIKE 21 software. A parametric study for different parameters which affect the residence time hence the water quality in lagoons, marinas, harbors and coastal basins was carried out to establish guidelines to improvement methods for water flushing of marinas and lagoons. Finite element conceptual computer models are applied to simulate and investigate the most important factors dominate the resident time and water exchange rate like tidal inlets characteristics (number-location-width), the shape of water body, basin dimensions and tidal variations. The boundary condition, water level variations used in simulations are collected based on the conditions of fishery ports and lagoons along Egyptian coastal line in Mediterranean and red sea. This study conducted a wide range of numerical simulation (more than 50 HD models) with different geometry and boundary conditions. The results showed that the square shape of water surface area is more efficient for small water body areas. While, as the area required increased, the rectangular water surface efficiency become closer. The inlet width and its location should be determined wisely to achieve the optimization for the usage of project. Finally, the results showed that as the level variations values increased, the maximum flood current velocities at the entrance increased. In addition, the flow spreading quality increased with higher water level values over the all water surface area regardless the water depth.