These data describe how microorganisms facilitate the cycling of reactive nitrogen in alpine ecosystems. Samples of water and sediment were collected from a longitudinal study of Loch Vale watershed in Rocky Mountain National Park in 2011 and 2012. Data presented include concentrations of NO3+ and NH4+ of surface waters and the relative abundance of nitrifying bacteria in both the water column and adjacent sediments. In addition we evaluated the isotopic signature (δ15N and δ18O) of NO3- from each surface water sample and weekly precipitation samples. Data on chemistry and microbial nitrification activity are also included from two additional nearby watersheds.