The prevailing paradigm to which most ecologists subscribe is that ecosystems are complex hierarchical systems. However, we ecologist model ecosystems with simple cause and effect algorithms (i.e., simple linear regression) which do not represent the complexities of the system. Path analysis is a means of converting conceptual models of ecosystem process and structure into mathematical formulas that can be evaluated statistically. We use path analysis to examine how a mountain watershed, Loch Vale, has been altered by climate change and atmospheric deposition over the last 25 years. Climate and nitrogen deposition controls on stream nitrate and terrestrial nitrogen cycling, specifically in the alpine tundra, are strong, while temperature control on Loch algal densities are weaker. Alpine microbial mineralization rates are more closely linked to algal blooms and nitrate concentrations in the Loch than sub-alpine forest mineralization rates. Our results confirm the Loch Vale ecosystem conceptual model that ecosystem types (i.e., alpine, forest, aquatic) need not be physically connected to have substantial influence on each other. Both tundra and forest moderate the effects of climate and nitrogen on mountain aquatic ecosystems, and the terrestrial alpine zone is a sensitive indicator of alterations in global climate and nitrogen cycles.