Since Jordan River NFH began operating in 1964, avian predators (including great blue herons) and mammalian predators (such as mink, raccoons, and opossums) have been responsible for the annual loss of 150,000 to 300,000 lake trout yearlings. The birds land on the raceways and cause a flight response in the trout. The fish smother each other, usually after running to the tail end of the raceway in attempts to escape predation. In this most recent example, the tail screen of the raceway became plugged with the suffocated fish, nearly causing it to fail.

That would have meant a loss of over 60,000 marked and tagged yearlings slated for stocking in Lake Huron's northern refuge. The 4,500 yearlings lost in January were part of an ongoing strain evaluation comparing the survival and wounding rates of two different lake trout strains in the presence of sea lamprey populations. This study also serves as an assessment of the sea lamprey control program by examining sea lamprey wounding rates on Superior-Marquette Domestic (now replaced with Superior-Traverse Island Wild) strain lake trout over time.

The Jordan River staff does employ various predator deterrent methods during their annual production cycles. However, the really frustrating consequence is that there is no way to tell how many fish are consumed by the predators until a final tally is completed just prior to their release. In 2002, an independent consultant retained by the Service to evaluate the Region 3 lake trout production hatcheries recommended a new production raceway enclosure be constructed at Jordan River NFH. This building would be designed to exclude predators, reduce sun exposure, eliminate snow removal difficulties and prohibit algal growth while providing an overall more efficient and safer rearing environment. USFWS Fisheries Regional Staff along with Jordan River NFH Staff are working toward implementation of the $1.2 million solution, the much needed enclosure.