Inadequate management practices for solid waste and wastewater are some of the main causes of eutrophication globally, especially in regions where intensive livestock, agricultural, and industrial activities are coupled with inexistent or ineffective waste and wastewater treatment infrastructure. In this study, a methodological approach is presented to spatially assess the trophic state of large territories based on public water quality databases. The trophic state index (TSI) includes total nitrogen, total phosphorus, chlorophyll A, chemical oxygen demand, and Secchi disk depth values as water quality indicators. A geographical information system (GIS) was used to manage the spatiotemporal attributes of the water quality data, in addition to spatially displaying the results of TSI calculations. As a case study, this methodological approach was applied to determine the critical regions for mitigating eutrophication in the state of Jalisco, Mexico. Although a decreasing trend was observed for the TSI values over time for most subbasins (2012–2019), a tendency for extreme hypereutrophication was observed in some regions, such as the Guadalajara metropolitan area and the Altos region, which are of high economic relevance at the state level. A correlation analysis was performed between the TSI parameters and rainfall measurements for all subbasins under analysis, which suggested a tendency for nutrient wash-off during the rainy seasons for most subbasins; however, further research is needed to quantify the real impacts of rainfall by including other variables such as elevation and slope. The relationships between the water quality indicators and land cover were also explored. The GIS methodology proposed in this study can be used to spatially assess the trophic state of large regions over time, taking advantage of available water quality databases. This will enable the efficient development and implementation of public policies to assess and mitigate the eutrophication of water sources, as well as the efficient allocation of resources for critical regions. Further studies should focus on applying integrated approaches combining on-site monitoring data, remote sensing data, and machine learning algorithms to spatially evaluate the trophic state of territories.