Little of the park was commercially logged. Commercial timber cutting began on westside, low-elevation forests in the 1860's. Rafts of logs were transported down Lake Chelan primarily for use as apple crates.
Timber was recognized as one of the major resources of the Cascades at an early date. Once the natural logjams that blocked the lower Skagit were cleared away in the 1870s, logging began to extend into the heart of the mountains. Logs were rafted down the river to be milled at settlements downstream. Logging also occurred in the Stehekin Valley. There were some mills in the valley that were used to mill lumber for local use. Most of the logs were rafted down Lake Chelan and used to make apple boxes. The lack of an adequate transportation system hindered early efforts to expand logging operations deep into the mountains. By far the most intensive logging that ever took place in the North Cascades occurred during the construction of the Skagit River hydroelectric project in the twentieth century.