Analysis of changes in functional groups of species and potential drivers of environmental change for protected areas across the world’s major tropical regions reveals large variation between reserves that have been effective and those experiencing an erosion of biodiversity, and shows that environmental changes immediately outside reserves are nearly as important as those inside in determining their ecological fate. Protected areas are a key component of tropical forest conservation strategy, but how well are they performing? These authors assemble a large data set from 60 protected areas across the globe, assessing 31 functional groups of species and 21 drivers of environmental change. They find that about half of the reserves are succeeding but half are experiencing substantial losses of biodiversity, driven as much by environmental change outside the reserves as by change within them. To protect what remains of these habitats, the authors suggest that it is vital to establish sizeable buffer zones around reserves, maintain substantial reserve connectivity to other forest areas and promote low-impact land uses near reserves. The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon1,2,3. With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses4,5,6,7,8,9. As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world’s major tropical regions. Our analysis reveals great variation in reserve ‘health’: about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.