Lakes and ponds are habitats of great human importance as they provide water for domestic, industrial and agricultural use as well as providing food. In spite of their fundamental importance to humans, freshwater systems have been severely affected by a multitude of anthropogenic disturbances, which have led to serious negative effects on the structure and function of these ecosystems. The aim of the present study is to review the current state of lake and pond ecosystems and to present a likely scenario for threats against these ecosystems for the time horizon of the year 2025. Predictions are based on a review of the current state, projections of long-term trends, for example in population and global climate, and an analysis of the trends in publications in the scientific literature during the past 25 years (1975–2000). The biodiversity of lake and pond ecosystems is currently threatened by a number of human disturbances, of which the most important include increased nutrient load, contamination, acid rain and invasion of exotic species. Analysis of trends suggests that older, well known threats to biodiversity such as eutrophication, acidification and contamination by heavy metals and organochlorines may become less of a problem in developed countries in the future. New threats such as global warming, ultraviolet radiation, endocrine disruptors and, especially, invasion by exotic species including transgenic organisms will most likely increase in importance. However, in developing countries where priorities other than environmental conservation exist, the threat of eutrophication, acidification and contamination by toxic substances is predicted to continue to increase. Although the future of biodiversity in lakes and ponds is seriously threatened, growing concern for environmental problems, implementation of new environmental strategies and administrations, and international agreements, are positive signs of changes that should improve the ability to manage old as well as new, yet undiscovered, threats.