Climate change has already impacted many species, with the effects expected to worsen in the future. The potential of species to adapt to climate change has been estimated various ways, including based on levels of standing genetic variation, presence of potentially beneficial alleles, and/or severity of environmental change. Kokanee salmon, the non-migratory ecotype of sockeye salmon (Oncorhynchus nerka) is culturally and economically important, and has already been impacted by the effects of climate change. To assess its climate vulnerability moving forward, we integrated analyses of standing genetic variation, genotype-environment associations and climate modeling based on sequence and structural genomic variation from 224 whole genomes sampled from 22 lakes from British Columbia and Yukon (Canada). We found that extreme temperatures, particularly warmest, had the most pervasive signature of selection in the genome and were the strongest predictors of levels of standing variation and of putatively adaptive genomic variation, both sequence and structural. Genomic offset estimates, a measure of climate vulnerability, were significantly correlated with higher increases in extreme warm temperatures, further highlighting the risk of summer heat waves that are predicted to increase in frequency in the future. Levels of standing genetic variation, an important metric for population viability and resilience, were not correlated with genomic offset. Nonetheless, our combined approach showed the importance of integrating different sources of information and genomic data to formulate more comprehensive and accurate predictions on the vulnerability of populations and species to future climate change.