This document discusses sources of uncertainty in paired watershed studies. It notes that watersheds cannot be replicated and it is difficult and expensive to treat replicate watersheds. Uncertainty analysis can be used to report statistical confidence. The document also provides details on a study that evaluated the impact of a whole tree harvest on nutrient removals and productivity by measuring the net hydrologic flux of calcium from two watersheds, W6 and W5, with W5 being harvested. Sources of uncertainty included precipitation interpolation and measurement, stream water measurements, and gaps in streamflow and chemistry data. A Monte Carlo approach was used to calculate uncertainty based on factors like watershed area. Potential sources of excess calcium in the harvested watershed W5