Wetlands provide ecological functionality by maintaining and promoting regional biodiversity supporting quality habitat for aquatic organisms. Globally, habitat loss, fragmentation and degradation due to increases in agricultural activities and urban development have reduced or altered geographically isolated wetlands, thus reducing biodiversity. The objective of this study was to assess the relative ecological function and integrity of natural ponds, excavated ponds and stormwater basins in the New Jersey Pinelands, located in the northeastern United States by comparing hydrologic conditions, water quality, pesticide concentrations (water, sediment and tissue) and wetland assemblages including amphibians. Twenty-four wetlands were selected based on surrounding land-use and sampled for a variety of abiotic and biotic variables. Abiotic and biotic wetland variables were similar between natural and excavated ponds, with notable differences between the ponds and stormwater basins. Natural and excavated ponds displayed characteristic Pinelands water quality (low pH, high organic carbon, and low pesticide concentrations), exhibited high ecological integrity and supported native ampbibians. Stormwater basins and degraded ponds surrounded by altered land-use exhibited degraded water quality (high pH, high pesticide concentrations) and were dominated by non-native and introduced plants and amphibians. Results from this study can broadly inform resource conservation strategies for amphibians and other communities with a diverse range of habitat requirements, particularly in areas where conservation and development are competing priorities. To conserve biodiversity in changing landscapes, wetlands with similar functionality and land-use characteristics need to be identified and managed to preserve water quality for species of conservation concern.