Assessments of future climate change impacts on ecosystems typically rely on multiple climate model projections, but often utilize only one downscaling approach trained on one set of observations. Here, we explore the extent to which modeled biogeochemical responses to changing climate are affected by the selection of the climate downscaling method and training observations used at the montane landscape of the Hubbard Brook Experimental Forest, New Hampshire, USA. We evaluated three downscaling methods: the delta method (or the change factor method), monthly quantile mapping (Bias Correction-Spatial Disaggregation, or BCSD), and daily quantile regression (Asynchronous Regional Regression Model, or ARRM). Additionally, we trained outputs from four atmosphere-ocean general circulation models (AOGCMs) (CCSM3, HadCM3, PCM, and GFDL-CM2.1) driven by higher (A1fi) and lower (B1) future emissions scenarios on two sets of observations (1/8º resolution grid vs. individual weather station) to generate the high-resolution climate input for the forest biogeochemical model PnET-BGC (eight ensembles of six runs).The choice of downscaling approach and spatial resolution of the observations used to train the downscaling model impacted modeled soil moisture and streamflow, which in turn affected forest growth, net N mineralization, net soil nitrification, and stream chemistry. All three downscaling methods were highly sensitive to the observations used, resulting in projections that were significantly different between station-based and grid-based observations. The choice of downscaling method also slightly affected the results, however not as much as the choice of observations. Using spatially smoothed gridded observations and/or methods that do not resolve sub-monthly shifts in the distribution of temperature and/or precipitation can produce biased results in model applications run at greater temporal and/or spatial resolutions. These results underscore the importance of carefully considering field observations used for training, as well as the downscaling method used to generate climate change projections, for smaller-scale modeling studies. Different sources of variability including selection of AOGCM, emissions scenario, downscaling technique, and data used for training downscaling models, result in a wide range of projected forest ecosystem responses to future climate change.