Western US forests represent a carbon sink that contribute to meeting regional and global greenhouse gas (GHG) targets. Forest thinning is being implemented as a strategy for reducing forest vulnerability to disturbance, including mortality from fire, insects, and drought, as well as protecting human communities. However, the terrestrial carbon balance impacts of thinning remain uncertain across regions, spatiotemporal scales, and treatment types. Continuous and in-situ long term measurements of partial harvest impacts to stand-scale carbon and water cycle dynamics are nonetheless rare. Here, we examine post-thinning carbon and water flux impacts in a young ponderosa pine forest in Northern Idaho. We examine in-situ stock and flux impacts during the 3 years after treatment as well as simulate the forest sector carbon balance through 2050, including on and off-site net emissions. During the observation period, increases in tree-scale net primary production (NPP) and water use persistence through summer drought did not overcome the impacts of density reduction, leading to 45% annual reductions of NPP. Growth duration remained constrained by summer drought in control and thinned stands. Ecosystem model and life cycle assessment (LCA) estimates demonstrated a net forest sector carbon deficit relative to control stands of 27.0 Mg C ha-1 in 2050 due to emissions