The effects of intensive banana production with high mineral-fertilizer application and of extensive pastures were compared regarding water quality in a lowland region of SE Mexico. We monitored NO, NO, and PO43– concentrations in groundwater (80 m depth), subsurface water (5 m depth), and surface water (open-ditch drainage) at monthly intervals for a one-year period. Irrespective of the land use, the NO concentrations in all water bodies were lower than the threshold value for drinking water and aquatic life. Particularly in areas with intense banana production, the NO contents in water exceeded the safety thresholds for drinking water of 1.0 mg L–1 (WHO, 2006) and aquatic ecosystems of 0.2 mg L–1 (OATA, 2008). Water from pastureland showed significantly higher PO43– concentration than that from the banana plantation, indicating a high risk of eutrophication. There is a need to provide recommendations for optimal time and amount of N application in commercial banana production and for limitation of P inputs in pasturelands to avoid further contamination of water bodies.