Context <p>Effective water quality management requires a comprehensive understanding of how landscape features influence nutrient enrichment. However, the lack of integrated, long-term studies linking Land Use Land Cover (LULC) changes in landscape patterns with both nutrient concentrations and loads limits the development of scalable water quality protection strategies.</p> Objectives <p>This study investigates how 60&#xa0;years of LULC change (1951–2010) influenced nitrogen and phosphorus loads and concentrations across 42 watersheds in Puerto Rico.</p> Methods <p>We integrated decadal LULC maps, nutrient monitoring data, and landscape metrics to quantify changes in composition and fragmentation at watershed, subwatershed, and riparian scales. Mixed-effects models evaluated both static LULC conditions and temporal change rates to identify spatial configurations most associated with water quality outcomes.</p> Results <p>We observed significant long-term reductions in nitrogen and phosphorus exports, coinciding with widespread agricultural abandonment and forest regeneration. Phosphorus declines were most strongly linked to subwatershed riparian changes particularly increased forest aggregation and decreased pasture dominance. Nitrogen reductions were more closely associated with broader riparian buffer conditions and urban development patterns, where dispersed urbanization contributed to elevated nitrogen loading. Forest configuration, especially its spatial aggregation, enhanced phosphorus retention.</p> Conclusions <p>Long-term shifts in land cover composition and configuration influenced nitrogen and phosphorus exports across Puerto Rico’s watersheds. Phosphorus reductions were driven by riparian forest aggregation, while nitrogen declines related to watershed-scale urban patterns. These results underscore the need for nutrient-specific, scale-aware strategies to guide land use planning in the tropics.</p>