The impacts of human-induced environmental change that characterize the Anthropocene are not felt equally across the globe. In the tropics, the potential for the sudden collapse of ecosystems in response to multiple interacting pressures has been of increasing concern in ecological and conservation research. The tropical ecosystems of Papua New Guinea are areas of diverse rainforest flora and fauna, inhabited by human populations that are equally diverse, both culturally and linguistically. These people and the ecosystems they rely on are being put under increasing pressure from mineral resource extraction, population growth, land clearing, invasive species, and novel pollutants. This study details the last ∼90 y of impacts on ecosystem dynamics in one of the most biologically diverse, yet poorly understood, tropical wetland ecosystems of the region. The lake is listed as a Ramsar wetland of international importance, yet, since initial European contact in the 1930s and the opening of mineral resource extraction facilities in the 1990s, there has been a dramatic increase in deforestation and an influx of people to the area. Using multiproxy paleoenvironmental records from lake sediments, we show how these anthropogenic impacts have transformed Lake Kutubu. The recent collapse of algal communities represents an ecological tipping point that is likely to have ongoing repercussions for this important wetland’s ecosystems. We argue that the incorporation of an adequate historical perspective into models for wetland management and conservation is critical in understanding how to mitigate the impacts of ecological catastrophes such as biodiversity loss.