The knowledge of flow hydrodynamics within the next decades is of particular importance in many practical applications. In this study, a methodological improvement has been made to the evaluation of the flow hydrodynamics under climate change. This research, indeed, proposes an approach which includes the methods that can consider the climate change impact on the flow in estuaries, gulfs, etc. It includes downscaling methods to project the required climate variables through the next decades. Here, two statistical downscaling methods, namely, Nearest Neighbouring and Quantile-Quantile techniques, are developed and implemented in order to predict the wind speed over the study area. Wind speed has an essential role in flow field and wave climatology in estuaries and gulfs. In order to make the proposed methodology computationally efficient, the flow in the estuary is simulated by a large-scale model. The finite volume triangular C-grid is analysed and shown to have advantages over the rectangular (finite difference) one. The dispersion relation analysis is performed for both gravity and Rossby waves that have crucial effects in oceanic models. In order to study the unstructured characteristic of the triangular grids, various isosceles triangles with different vertex angles are considered. Moreover, diverse well-known second-order time stepping techniques such as Leap-Frog, Adams-Bashforth and improved Euler are studied in combination with the C-grid semi discrete method. The fully discrete method is examined through several numerical experiments for both linear and non-linear cases. The results of the large-scale model provide the boundary conditions to the local coastal model. In order to model the flow over a local coastal area, a well-balanced positivity preserving central-upwind method is developed for the unstructured quadrilateral grids. The quadrilateral grid can effectively simulate complex domains and is shown to have advantages over the triangular grids. The proposed central-upwind scheme is well-balanced and preserve the positivity. Therefore, it is capable of modelling the wetting and drying processes that may be the case in many local coastal areas. It is also confirmed that the proposed method can well resolve complex flow features. The local model incorporates the outputs of the downscaling and large-scale flow models and evaluates the flow hydrodynamics under changing climate.