Species inhabiting the North American west coast intertidal must tolerate an extremely variable environment, with large fluctuations in both temperature and salinity. Uncovering the mechanisms for this tolerance is key to understanding species’ persistence in extreme and changing environments. We tested for differences in baseline salinity tolerance and differences in the plasticity of salinity tolerance between populations of the splashpool copepod Tigriopus californicus from locations in northern and southern California known to differ in temperature, precipitation, and humidity. We also compared phenotypic differences between populations to the their transcriptomic responses to salinity stress. The southern population showed a faster recovery under hyperosmotic stress, and this response was accompanied by a greater transcriptomic response to high salinity. Northern and southern copepods did not differ in their initial response to high salinity, but southern copepods still recovered more quickly than northern copepods. Both populations responded similarly to low salinity in terms of the number of differentially expressed genes, however the northern population showed constitutive up-regulation of the low salinity response under ambient conditions, a putative mechanism for the greater initial tolerance of this population to low salinity stress. Transcripts differentially regulated under salinity stress were enriched for ‘amino acid metabolism’ and ‘ion transport’ annotation categories, supporting previous work demonstrating the accumulation of free amino acids is important for osmotic regulation in T. californicus. Our results suggest that southern copepods have higher phenotypic plasticity to osmotic stress and may be better adapted to salinity shifts driven by climate change and anthropogenic disturbance.