Many high-elevation regions in the western USA are protected public lands that remain relatively undisturbed by human impact. Over the last century, however, nonnative trout and cattle have been introduced to subalpine wetland habitats used by sensitive amphibian species. Our study compares the relative importance of cattle and trout impact on amphibian assemblages, abundance, and occupancy within a broader context of high-elevation environmental variables. We evaluated amphibian species richness and abundance across 89 subalpine wet meadow sites in the Klamath Mountains of Northern California, USA. At each wet meadow we also measured environmental characteristics including wilderness designation, elevation, meadow size, number of pools, distance to nearest lake, presence of nonnative trout, and impact of cattle. Cluster analysis found amphibian assemblages fell into three distinct groups, and ordination suggested the number of pools, elevation, and presence of nonnative trout are significant site variables associated with species groups in wet meadows. Individual species differed in population response to environmental characteristics. Regression trees and occupancy models indicated that the most-important variables associated with the population size and site occupancy of individual amphibian species are nonnative trout, wilderness area designation, the number of pools, and the distance to the nearest lake. While nonnative trout exhibited a strongly negative correlation with amphibian assemblages, abundance, and occupancy, cattle impact was only weakly associated with occupancy and abundance of some species.