Centrarchids (sunfish and bass species) and Bullfrogs (Lithobates catesbeianus) have been introduced into aquatic systems around the world and have the potential to negatively impact native fish and anurans. We surveyed fish and anuran assemblages from 26 impoundments in the New Jersey Pinelands, USA. We excluded non-native species and used ordination analysis to generate four native-species community gradients based on native-fish and anuran presence–absence and abundance data. All four community gradients paralleled an increase in the percentage of upstream-altered land (development and upland agriculture) and an increase in either non-native-centrarchid richness or abundance. Based on presence–absence and abundance data, native-fish and native-anuran assemblages, including restricted species (those generally limited to the Pinelands region) and widespread species (those widely distributed in New Jersey), differed between impoundments with and without non-native centrarchids. Compared to widespread species, the greatest differences between impoundment types were found for restricted species. Three non-native-frog species, including Bullfrogs, were associated with degraded impoundments that supported non-native fish. Our results demonstrate that watershed conditions and native fish and anuran assemblages differ between impoundments with and without non-native centrarchids, and suggest that some restricted species may be especially vulnerable to impacts from watershed disturbance and non-native species. Our findings support the idea that the environmental resistance associated with intact water-quality conditions may help prevent the invasion of non-native fish and anurans. We recommend that land-use activities that degrade water quality and reduce invasion resistance be avoided in unaltered watersheds to conserve native-fish and native-anuran community integrity.