The approval of the current Bathing Water Directive (Directive 2006/7/EC) set the necessity to define the bathing water profile. The goals established in the definition of the profile are: (i) to know the processes that determine the concentration of bacteriological indicators in the aquatic environment, (ii) to obtain relationships between the cause of pollution and its effects, and (iii) to evaluate the fulfilment of the Directive and to set the Quality Monitoring and Assessment Program, according to the bacteriological characteristics of the bathing water. In this paper an approach to elaborate the bathing water profile and its application to several bathing waters located in Santander municipality (North Spain) is shown. The methodology involves the assessment of advection, diffusion and reaction processes of bacteriological organisms in the aquatic environment by using mathematical models and the selection of an indicator to evaluate the probability to exceed the bacteriological concentrations established in Directive 2006/7/EC, which is useful for the ‘source apportionment’ assessment. In the definition of the bathing water profile we have considered the sanitation system operating under normal conditions, which includes storm water overflows, uncontrolled discharges and the discharge produced when the pumping system of the wastewater breaks. Finally, according to the bacteriological characteristics of the bathing water it is necessary to develop the Quality Monitoring and Assessment, which has been done taking into account the requirements established in Directive 2006/7/EC and the uncertainties detected in such a method regarding the number of samples to be considered.