This research addresses the challenge of assessing ecosystem services, ecosystem condition, and agricultural externalities in a Latin American socio-ecological context, where primary production is both a major economic activity and a pressure on ecosystems. In Uruguay, the intensification of agriculture and livestock farming has raised concerns about nutrient-related externalities affecting water and soil quality. Although the System of Environmental and Economic Accounting (SEEA)—Ecosystem Accounting framework is used for better ecosystem management, it does not explicitly represent externalities. Using the Santa Lucía sub-basin in Uruguay (supplying water to 60% of the population) as a case study, this research combines the Soil and Water Assessment (SWAT) Tool with ecosystem accounting principles to assess ecosystem services, ecosystem condition, and externalities. Model outputs are used to compile partial ecosystem accounts in physical terms, integrating spatially explicit indicators. Results show that nutrient losses to surface waters, interpreted as agricultural externalities, are predominantly driven by diffuse sources associated with croplands and dairy systems and shaped by hydrological connectivity. Despite data and model-related uncertainties, the approach supports hotspot identification and the spatial targeting of interventions and provides the basis for future monetary assessment, illustrating how hydrological modeling can complement ecosystem accounting in data-scarce contexts.