Dam impacts on aquatic life
If irrigation districts open dams and flood the river in summer, then vegetation along the river banks erodes. This kills local fish and other aquatic species like the Oregon spotted frog, which is close to extinction. There have been many lawsuits filed to protect endangered species. Yet the USFWS can protect irrigation districts from species-protecting lawsuits—even if some animals go extinct due to over-irrigation. These animals include three federally listed species, the Oregon spotted frog, bull trout, and steelhead, and one currently unlisted species, sockeye salmon.  The Deschutes Basin Board of Control made a Habitat Conservation Plan that commits them to water conservation for the next three decades.

Drought and wildfire
With regards to the last 20 years of drought in Central Oregon, this region does not have decades to waste because of climate change. Six districts all compete for water, and this is exacerbated by a 10-year trend of drought which is widely believed to be caused by climate change. The Deschutes River Conservancy and local irrigation districts have come up with a variety of water conservation solutions to address the challenges of drought and over-appropriation. These include piping the canals, upgrading individual farms and ranches efficiently, and paying property owners to give their water back to the river or to other farmers growing food (water marketing). There has been more emphasis recently on the importance of Western water quantity given USDA's roles in the National Drought Resilience Partnership and the new Water Sub-cabinet.

Water quality
The U.S. Department of Agriculture has hosted virtual meetings seeking input about water quantity in the West in the context of programs its Natural Resources Conservation Service offers.  Hearing from stakeholders is needed to address water quantity issues in the western U.S. Many water conservation strategies have been designed and implemented to gradually increase the flows in the upper Deschutes in the winter months to 400 cubic feet per second over the next 20 years.

Central Oregon Irrigation District, the largest district in Central Oregon, expects to pour $100 million over the next decade to pipe a significant portion of its open canals and ditches to replace old canals, which are so porous they lose half the water that entered before reaching its destination.  The infrastructure system needs to be updated, but building pipes is more expensive and time-consuming than prioritizing on-farm conservation and water marketing. Eight irrigation districts take water from the river through elaborate irrigation canals.  Water comes down from the mountains and is captured in three reservoirs starting in November, including Wickiup, Crane Prairie, and Crescent reservoirs. The human-made lakes store water through the winter and spring. Then, irrigation districts release the dams in the summer so property owners can use the water to maintain their farms and businesses. The problem started 120 years ago when the river was massively over-appropriated because the belief was that water would never be scarce in this region. As part of a Water Smart grant, loan money to do on-farm improvements as a commitment to incentivizing the farmers to do better. If irrigators meet water-saving targets, they will receive protection from lawsuits protecting endangered species.

Klamath tribes, the senior water rights holders in the region, have requested shut-offs to preserve water for ecological reasons — even though some tribal members are also adversely affected, Oregon has historically allowed more people to claim more water rights than the water supply could support.  At the turn of the 20th Century, settlers claimed water on a first-come, first-serve basis. These agreements with the state were attached to a tract of land, not a person. This means people who run hobby farms, golf courses, and some agriculture operations closer to Bend have first or "senior" rights to the water because this area was settled a few years before farms farther north, in Madras and Culver. Senior water rights holders can order junior holders to shut off water until the senior gets their full allotment. As Bend developed into a hot destination for real estate and tourism, many farms were sold off and turned into hobby ranches, which is potentially unfair to privileged property owners who are raising animals for fun over commercial agriculture operations.

With insufficient financial resources, The Oregon Water Resources Department can only inspect about 30% of the 3,000 new wells drilled in Oregon each year, which has raised concerns about construction deficiencies. Roughly 10% of wells are estimated to have construction or paperwork deficiencies. Improperly sealed wells could cause contaminants from the surface to seep into the groundwater, while improperly drilled wells could drain water from other nearby aquifers. There is a push to impose new requirements on well drillers to protect groundwater supplies. The Oregon Water Resources Department is considering a "legislative concept" that would require drillers to provide evidence of their welding skills and would narrow the time they must notify the agency of new installations.