Water quality assessment in rivers or coastal areas is an important contribution to satisfy human basic needs, to promote economic development and to protect aquatic ecosystems and species. The main hydrological, hydraulic, chemical and biological processes and their dynamic linkage with human activities such as land and water use and pollution must be known or predictable. Chemicals speciation in water affects impacts on public health and ecosystems. Water pollution prevention and remediation minimizes the impacts of water use on the natural environment. The water quality impacts of human activities as well as possible mitigation measures have to be considered in different socio-economic contexts. The identification of domestic and industrial pollution sources, the knowledge of the transport and dispersion characteristics of pollutants as well as hydraulic, hydrological and water quality modeling tools are relevant contributions to river basin management strategy.