Karst aquifers are a major source of drinking water with intrinsic features that increase the pollution risk from anthropogenic and natural impacts. In Yucatan, Mexico, groundwater is the sole source of drinking water, also acting as receptor of untreated wastewater due to the low regional coverage of sewer systems. To protect karst groundwater, vulnerability methodologies are widely used. Worldwide, multiple karst vulnerability schemes have been developed and tested; however, none of these consider pollutant residence time or pollutant concentration as core parameters to estimate vulnerability. This work aims to define important considerations regarding the behavior of nitrates (NO₃) in a real scenario, to be included in a new integrated vulnerability method. This work has two main objectives: to set up a groundwater model to depict as close as possible the groundwater behavior of the Yucatan karst system, and to introduce a transport model to estimate the behavior of a pollution plume. Model outcomes suggest that pollutants have a short residence time, reaching the coast in the north after 3 years. Well fields are also affected by pollution at variable NO₃ concentrations. Results can be further discretized to establish a base and to include these parameters as part of a new integrated groundwater vulnerability approach.