Rising mean and variance in temperatures elevate threats to endangered freshwater species like the lake sturgeon, Acipenser fulvescens. Previous research has demonstrated that higher temperatures in early development result in physiological consequences for lake sturgeon populations throughout Manitoba, Canada, with alteration of metabolic rate, thermal tolerance, transcriptional responses, growth, and mortality. In the present study, we acclimated lake sturgeon from northern and southern populations within Manitoba to current and future projected environmental temperatures of 16, 20, and 24C for 30 days, and measured gill transcriptional responses using RNAseq. We found population-specific and acclimation-specific responses to the thermal treatments, as well as conserved molecular responses between northern and southern sturgeon populations. Expression profiles revealed a gradient in transcriptional responses consistent with acclimation temperature, with a higher number of differentially expressed transcripts observed in the southern compared to the northern lake sturgeon population as temperatures increase, indicating enhanced transcriptional plasticity. Overall lake sturgeon populations responded to thermal acclimation by upregulating the expression of transcripts involved in transcriptional and translational regulation, mitochondrial function, pathogen responses, and DNA damage, as well as genes associated with pre- and post-transcriptional processes (i.e., methylation, alternative splicing). Further, both populations upregulated transcript expression related to cell structural damage as temperatures increased to 20C, but the northern population also responded with increases in damage signaling and recruitment of mitochondrial processes involved in ATP production. Ultimately, these transcriptional responses highlight molecular consequences of increasing temperatures for divergent lake sturgeon populations during vulnerable early developmental periods and the critical influence of transcriptome plasticity on acclimation capacity.