Development in southwest Puerto Rico, as in many areas of the Caribbean, is outpacing the ability of upland flora, salt flats, and mangroves to capture sediments and intercept and transform nutrients. A comparative study to examine the effects of development on near-shore water quality in La Parguera, Puerto Rico, was initiated in 1998. Total suspended solids were significantly higher in the vicinity of developing areas compared to reference areas. Chlorophyll-a measurements near of the wastewater treatment plant averaged two times the level of other areas. The overall average concentrations of copper, chromium, nickel, and zinc in sediments collected from salt flats exceeded values reported to cause impairment of biological systems. Marine sediments near more developed locations had the highest metal concentrations, suggesting a greater transport in this area. Natural resources are the primary attraction in this area; therefore, protection of near-shore resources should receive greater attention in land use planning.