We review known and hypothesized effects of nitrogen (N) deposition owing to human activities on the chemistry, organisms, and ecosystem processes of remote oligotrophic freshwaters. Acidification is the best-known effect of N deposition on water chemistry, but additional effects include increased nutrient availability and alteration of the balance between N and other nutrients. Our synthesis of the literature, framed in a comprehensive model for the effects of N deposition on natural ecosystems, shows that all these effects can reduce biological diversity and alter ecosystem processes in remote freshwaters. N deposition is projected to grow worldwide in the near future and will interact with other global changes. Present effects on these fragile ecosystems may be only early signs of more radical impacts ahead.