Given the unique setting of being a watershed, the water quality issues in the Willamette River Basin are manifold. In 1991, the Willamette River Basin was among the first 20 rivers selected for study under the National Water-Quality Assessment (NAWQA). Some of the water quality problems include the following:
- Biological degradation
- Erosion of soils due to changes in land use
- Evaluation of surface- and ground-water flow
- Trace organic compounds and trace elements in surface and ground water and, perhaps, naturally occurring radon in ground water
The geology of the Willamette River Basin can probably be best described as a large "trough" or low area. The Oregon Water Resources Department has identified four regional hydrogeologic units: (1) the low-yield bedrock unit; (2) the Columbia River Basalt unit; (3) the basin-fill sediment unit; and (4) the Willamette Silt unit. The Columbia River Basalt is the most prolific aquifer.