Effectiveness of Fish Screens to Reduce Entrainment of Threatened Salmonids into Irrigation Systems on the Lemhi River, Idaho

Unscreened irrigation diversions are suspected to pose a threat to the survival of pre-smolt and smolt Chinook salmon Oncorhynchus tshawytscha, steelhead O. mykiss, and other migratory fish. Fish screens designed to keep downstream migrating fish from becoming entrained into irrigation ditches have been installed on 98 diversions in the Lemhi River subbasin, a tributary to the upper Salmon River in Idaho. All screens constructed and installed since the early 1990’s have been designed to meet National Marine Fisheries Service criteria for screening juvenile salmonids. These criteria provide a means to safely return fish that enter irrigation ditches to the main river channel through a bypass pipe. The Idaho Department of Fish and Game’s Anadromous Fish Screen Program has been evaluating fish screen bypass efficiency in the Lemhi River since 2003. The objectives of the study were: 1) document the entrainment rate of juvenile Chinook salmon through monitored fish screen bypass pipes on the Lemhi River 2) document the correlation between the timing of the downstream migration of juvenile Chinook salmon and the Lemhi River hydrograph, 3) and document the correlation between the rate of entrainment and Lemhi River discharge when instream flows are significantly reduced by irrigation withdrawals. Objectives were met by monitoring fish screen bypass pipes for downstream migrating anadromous smolts and presmolts that had been implanted with Passive Integrated Transponder (PIT) tags in the upper Lemhi River subbasin. Two to four automated PIT tag interrogation systems were installed on various bypass pipes for monitoring throughout the irrigation season from 2003 through 2010 to measure entrainment rates. The highest rate of detection of bypassed PIT tagged Chinook salmon occurred during the smolt migration, with rates varying from 6% up to 34%. A strong negative correlation was noted between the volume of flow measured in the Lemhi River and the rate of entrainment.