Effective management of water resources is vital in civil engineering, encompassing natural and urban water systems. This chapter introduces the application of MATLAB in hydrology and water resources engineering, offering engineers the tools to model, simulate, and optimize the behavior of water within various systems. The chapter covers essential topics such as the flow of water in open channels and pipes, water distribution networks, and flood risk analysis. MATLAB’s computational capabilities are explored in detail, providing insights into solving complex hydraulic equations and simulating water flow through channels and networks using key methods like the Saint-Venant and Darcy–Weisbach equations. Practical examples are provided to demonstrate how MATLAB can be used to model real-world problems, such as optimizing water resource allocation, simulating flood risks, and analyzing water distribution networks for both efficiency and sustainability. The chapter also delves into advanced topics like hydraulic modeling, pipe network optimization, and water quality simulations, illustrating the vital role of computational analysis in designing reliable water infrastructure. By mastering these techniques, civil engineers will be well equipped to develop solutions that ensure the sustainable management of water resources.