Part of the assessment of each stream reach was to document factors that were affecting stream health at the time of the assessment, or were likely to be a significant threat in the near future. While the threats varied from reach to reach, the reoccurrence of many of the threats was notable. Our “top ten” threats for the watershed as a whole are listed below, roughly in the order of their importance based on the number of reaches where each was documented:

1. Dewatering: Due both to trans-basin water diversions and in-basin diversions, primarily for agriculture. Loss of water and reduced flow decreases the stream’s ability to carry sediment and maintain good physical habitat for fish and stream insects, and it reduces the effect of dilution on waterborne pollutants.
2. Recreational Disturbance: Primarily from fishermen and rafters, causing trampling of riparian vegetation and development of “social” trails that degrade riparian habitat and destabilize stream banks. 
3. Road Disturbance: Especially in narrower tributary valleys, the presence of roads and adjacent rip-rapped stream banks has effectively channelized the streams and eliminated riparian vegetation. 
4. Residential and Commercial Development in Riparian Zone: This includes building construction and landscaping “to the water’s edge”, eliminating riparian vegetation, often requiring bank armoring, or rip-rapping, with boulders to reduce erosion. 
5. Noxious Weeds: Land disturbance and removal of native vegetation are prime causes for the invasion of noxious weeds, such as Canada thistle, nightshade, poison hemlock, houndstongue, and leafy spurge, which often prevent the re-establishment of native vegetation and do little to stabilize stream banks.
6. Livestock in the River and in Riparian Zones: Cattle trample riparian vegetation, contribute to eroding stream banks, and degrade in-stream habitat for aquatic insects, plus, their manure contributes to nutrient enrichment of the stream water. 
7. Nutrient Enrichment: Nutrients, such as nitrates, ammonia, and phosphates, that come from a variety of sources such as private septic systems, municipal waste treatment plants, fertilizers from lawns and golf courses, and agriculture, often lead to excessive algal growth in the stream, and in extreme situations can reduce dissolved oxygen and cause fish mortality. 
8. Agricultural Elimination of Riparian Vegetation: In wider floodplain areas, riparian vegetation has been replaced by hay meadows. This has often led to stream bank erosion, down cutting of the river channel, and isolation of floodplain soils from inundation during spring floods. 
9. Stream Channelization: In many places, the stream channel has been confined and often straightened, and the banks typically armored with boulders to prevent erosion. While this practice might indeed prevent erosion in channelized areas, stream energy during spring floods is poorly dissipated and often contributes to erosion and down cutting farther downstream. 
10. Elimination of Beaver Ponds: Beaver ponds trap sediment and help dissipate the stream’s energy, thus preventing erosion. Also, the natural “boom and bust” cycle of beaver activity in the floodplain contributes to a more diverse riparian habitat, which in turn increases wildlife diversity.

Vegetation removal in this golf community has destabilized stream banks, reduced shade that maintains cooler water temperatures and eliminated both aquatic and riparian wildlife habitat. Boulder rip-rap on the banks channelizes stream energy toward the next unprotected area downstream.	Cattle degrade water quality and destroy riparian habitat. Some of the ranches in the valley fence their livestock out of the riparian zone and allow access to water only at specific places, which results in a much healthier river system.