Nonnative brook trout exist in high numbers in the Upper Malheur. The introduced fish poses serious threats to the long term viability of bull trout because of its ability to outcompete and hybridize with the native. Resource competition and hybridization between the two species is documented in the Upper Malheur. Brook trout threats, along with other environmental and anthropogenic factors, have imperiled the native in the Upper Malheur and led to the population being classified as having a “high risk” of extinction. Recovery Criteria for the Malheur Recovery Unit cites stable or increasing abundance trends in both local populations and the reestablishment of connectivity between the separated populations as actions necessary to achieve delisting. However, it has also been deemed necessary to achieve a reduction or elimination of threats from brook trout interaction in the Upper Malheur prior to restoration of passage. Full recovery of Malheur River bull trout is therefore contingent upon minimizing the threats posed by brook trout interaction in the basin. Brook trout are a primary limiting factor to bull trout recovery.

Reducing the effect of brook trout on bull trout is strategized under Objective 4.1 of the Subbasin Plan. The task of implementing a feasible and biologically supportable brook trout removal project received priority one designation under the plan for the Malheur Recovery Unit (Task 2.5.1). According to Task 6.1.2 for the recovery unit, BPT proposes to take the lead in implementing this effort. The draft Malheur River Bull Trout Implementation Strategies and recent draft updates to the USFWS Recovery Plan also identifies reduction of brook trout populations as a priority limiting factor necessitating immediate action.

Implementation of mechanical methodology to control brook trout in the Malheur River began through this project in FY2011.  BPT considers current use of mechanical methodology and baseline data collection as “Phase I” of suppression efforts, as approved in the FY2012 Categorical Review of Resident Fish projects.  "Phase II" will likely consist of a prioritized and tiered approach to velocity barrier installation and chemical treatment of the seventy plus miles of tributary habitat affected by brook trout.  “Phase II” will be contingent upon the results and baseline establishment in “Phase I” (e.g., barrier site selections, success of electrofishing/weir removal efforts, etc.), and the continued collaboration between state and federal agencies and BPT.

These efforts coincide with additional projects funded by other sources: use of eDNA to detect changes in abundance of brook trout and to monitor resulting trends in bull trout (Bureau of Reclamation funding), removal of brook trout in seed source areas (Bureau of Reclamation Funding); installation of a PIT tag array at the confluence of the two tributaries currently targeted for brook trout removal (U.S. Fish and Wildlife Service funding); development of NEPA analysis for long term treatment of High Lake (U.S. Fish and Wildlife Service Tribal Wildlife Grant); empirical investigation of the complete range of brook trout in the basin in order to evaluate eradication options (U.S. Forest Service Funding).  This project also has attracted substantial in-kind contributions through interagency collaboration.

All work elements were approved in the FY2013-2017 Categorical Review by NPCC.