The main objective of the present study is to make a step forward in the assessment of mixing zones of single-port industrial discharges in estuaries by developing and implementing a stepped methodology according to the significance of the considered discharge. Thereby, this methodology establishes where a mixing zone is required and determines its size and acceptability for each point discharge based on numerical models and mathematical tools. Thus, in this thesis a “Stepped Approach” has been developed to document the policy decision tree (methodology) that may be adopted by Member States and/or Industries when setting Mixing Zones (MZs) under Directive 2008/105/EC and Directive 2013/39/EU. The structure of the thesis is organized in six chapters as follows: - Chapter 1. Introduction. This chapter has introduced the reader in all other chapters of the thesis. Firstly, the motivations for research, explaining their importance and the reasons that led to the development of this thesis, are displayed. Secondly, the general aim of the thesis is presented and, finally, the organization of this thesis is explained. - Chapter 2. State of the Art. With the general aim in mind, a literature review is carried out in this chapter in order to evaluate the different methodological approaches used in daily practice around the globe, to state the contemporary issues in estuarine physics (hydrodynamics and mixing) and, finally, to gather the available numerical tools used to study estuarine hydrodynamics and mixing. This review highlights the strengths and deficiencies found in current approaches and allows the definition of the final objectives of the present work. - Chapter 3. Overall Methodology. In this chapter, the developed methodology, involving five steps, has been described. In Step 1, we collect the required information about the study area and the toxicant discharges. Step 2 identifies the significance of the discharge or discharges in the study zone. Next, Step 3 evaluates the effect generated by discharges and delimitates MZs from a simplified calculation that takes into account fixed conditions. Step 4 evaluates the effect generated by discharges and delimitates MZs during the driest year according to the river flow. Finally, in Step 5, we ’reevaluate’ the effect generated by discharges and ’redelimitate’ MZs according to a real case of dilution taking into account the variability of the environmental forcings. - Chapter 4. Numerical Tools. In this chapter, a review of the used numerical models and all the self-developed mathematical tools for integrating, transferring, communicating and plotting the required and obtained information along the overall methodology is presented. - Chapter 5. Results: Application to Suances Estuary. The implementation/application to Suances Estuary of the developed methodology in Chapter 3, using the proposed numerical tools described in Chapter 4, is presented. - Chapter 6. Conclusions and Future Research Topics. At the end of the document the conclusions of the present work are presented together with some proposals for future research topics that may complement the present study and the proposed methodology. Lastly, all the contributions made by this thesis were itemized.