•Sockeye salmon chronic exposure to clothianidin.•(0.15, 1.5, 15, 150 μg/L) did not decrease survival, hatching, growth or deformities.•Low level clothianidin (0.15 μg/L) increased 17β-estradiol levels in sockeye salmon swim-up fry, but testosterone was unaffected.•Liver glucocorticoid gene expression was reduced after 150 μg/L clothianidin exposure in sockeye salmon swim-up fry. One of the categories of environmental contaminants possibly contributing to declining sockeye salmon (Oncorhynchus nerka) in the Fraser River, British Columbia, Canada is pesticides. In this 4-month study, the effects of environmentally relevant concentrations of a waterborne neonicotinoid, clothianidin (0.15, 1.5, 15 and 150 μg/L), on embryonic, alevin and early swim-up fry sockeye salmon derived from four unique genetic crosses of the Pitt River, BC stock were investigated. There were no significant effects of clothianidin on survival, hatching, growth or deformities, although genetic variation significantly affected these endpoints. Clothianidin caused a significant 4.7-fold increase in whole body 17β-estradiol levels in swim-up fry after exposure to 0.15 μg/L, but no effects were observed on testosterone levels. In addition, hepatic expression of the gene encoding glucocorticoid receptor 2 was also impacted at the highest concentration of clothianidin tested, and was found to be ∼4-fold lower compared to the sockeye reared in control water. These results indicate additional examination of clothianidin and its effects on salmonid gonad development and the reproductive and stress endocrine axes in general, is warranted.