Forested ecosystems in the southeastern United States are currently undergoing an invasion by the hemlock woolly adelgid (HWA). Previous studies in this area have shown changes to forest structure, decreases in canopy cover, increases in organic matter, and changes to nutrient cycling on the forest floor and soil. Here, we were interested in how the effects of canopy loss and nutrient leakage from terrestrial areas would translate into functional changes in streams draining affected watersheds. We addressed these questions in HWA-infested watersheds at the Coweeta Hydrologic Laboratory in North Carolina. Specifically, we measured stream metabolism (gross primary production and ecosystem respiration) and nitrogen uptake from 2008 to 2011 in five streams across the Coweeta basin. Over the course of our study, we found no change to in-stream nutrient concentrations. While canopy cover decreased annually in these watersheds, this change in light penetration did not translate to higher rates of in-stream primary production during the summer months of our study. We found a trend towards greater heterotrophy within our watersheds, where in-stream respiration accounted for a much larger component of net ecosystem production than GPP. Additionally, increases in rhododendron cover may counteract changes in light and nutrient availability that occurred with hemlock loss. The variability in our metabolic and uptake parameters suggests an actively-infested ecosystem in transition between steady states.