Since time immemorial, aboriginal people of the Confederated Tribes of the Warm Springs Reservation of Oregon (CTWSRO) have harvested fall Chinook salmon (Oncorhynchus tshawytscha) for subsistence, ceremonial, and medicinal purposes. Not only is this species culturally significant, but it also has a high economic and recreational value to non-Indians. The CTWSRO has co-management authority of fisheries resources in the Deschutes River with Oregon Department of Fish and Wildlife (ODFW). Deschutes River fall Chinook are an indicator stock managed under the Pacific Salmon Treaty (PST) and is used to determine ocean harvest. The CTWSRO has obligations to provide reliable escapement estimates to the United States Chinook Technical Committee, the body that implements the PST. The ODFW has obligations to provide escapement estimates to the Columbia River Compact, which sets in-river harvest.

Much of the data collection for fall Chinook in the Deschutes Basin has centered on providing escapement estimates of returning adults. The CTWSRO is particularly interested in population trends upstream of Sherars Falls as fall Chinook above this point are nearly all of the reporting group Deschutes River summer/fall Chinook. From Sherars Falls to the mouth, they are mixed stock, primarily upper Columbia River summer/fall stock. The CTWSRO had been working with ODFW to complete aerial surveys for fall Chinook redds. Aerial redd surveys have been conducted in index reaches and/or from the mouth to Pelton Re-regulating Dam (Rkm, 161) since 1977. This BPA contract will no longer be used to fund this effort as the CTWSRO views this as a matter for the state to report whole river escapement whereas we are interested in the mark-recapture estimate of Deschutes River fall Chinook upstream of Sherars Falls, which is a better representation of population trends of Deschutes River stock than the whole-river estimate. Because of poor visibility and superimposition of redds downstream of Pelton Re-regulating Dam at times aerial redd counts may be imprecise, which adds a source of error to the whole-river escapement estimate. The CTWSRO will continue to work with ODFW on the mark-recapture effort which involves implanting returning adult fall Chinook with uniquely numbered Floy tags at Sherars Falls and recapturing tagged fish through a carcass survey from Pelton Re-regulating Dam to Trout Creek (rkm 141).

In an effort to determine where Deschutes River fall Chinook were harvested, the CTWSRO implanted coded-wire tags (CWT)into juvenile outmigrants between 2002 and 2009. The lower Deschutes River, downstream of Sherars Falls, was surveyed for carcasses that may have been implanted with CWTs. The lower river carcass survey was discontinued after 2016 as no more returning adults were expected.

In 2011, the CTWS began a study to determine juvenile and adult fall Chinook migration patterns as upwards of 25,000 juveniles were implanted with PIT tags until 2017. Using PIT tag arrays at mainstem dams, the PIT tag trawl in the estuary and arrays at the mouth of the Deschutes and Sherars Falls, there were many opportunities for detection but far fewer than expected tagged fish were detected. Through this effort, detection efficiency and survival was studied. As part of annual PIT tagging, approximately 5,000 tissue samples were collected each year in 2016 and 2017. These are archived and will be of interest for genetic analysis to determine the frequency of the gene that control cold-water tolerance, Calmodulin, in returning fall Chinook to compare differential survival of fish expressing this gene. This is of interest as fall Chinook, prior to construction of Pelton-Round Butte Hydrologic Complex in the early 1960s, determined from archived scale samples, showed low frequency of expressing Calmodulin. After operation of the Hydro-Complex when cold water was withdrawn from the bottom of the reservoir and released downstream, the opposite was seen; high frequencies of Calmodulin expression. After the select-water withdrawal became operational in 2010 and water was mixed to mimic the historic thermal regime, fall Chinook began reverting back to lower frequency of Calmodulin expression. From an ecological point of view, we would like to have enough of those 10,000 PIT tagged fall Chinook with which we have tissue samples to investigate whether the original expression of the coldwater tolerance gene is associated with higher survival. However, the PIT tagging of juvenile fall Chinook was suspended after 2017 due to low number of returning PIT tagged fish that were detected. In addition, CTWS chose to direct staff to higher priority projects in response to declining spring Chinook and uncertainty research in summer steelhead.

In 2019 - 2020, study objectives are to:
-Record PIT tag detections at antenna arrays at the Deschutes River mouth and Sherars Falls;
-Assist ODFW with marking returning fall Chinook at Sherars Falls, and;
-Conduct carcass surveys for mark-recapture escapement estimates and to recover PIT/CWT/Floy tags.