Populations that tolerate extreme environmental conditions with frequent fluctuations can give valuable insights into physiological limits and adaptation. In some estuarine and marine ecosystems, organisms must adapt to extreme and fluctuating salinities, but not much is known how varying salinities impact local adaptation across a wide geographic range. We used eight geographically and genetically divergent populations of the intertidal copepod Tigriopus californicus to test if northern populations have greater tolerance to low salinity stresses, as they experience greater precipitation and less evaporation. We used a common garden experiment approach and exposed all populations to acute low (1, 3ppt) and high (110, 130ppt) salinities for 24 hours, and a fluctuation between baseline salinity and moderate low (7ppt) and high (80ppt) salinities over 49 hours. We also performed RNA-sequencing at several time points during the fluctuation between baseline and 7ppt to understand the molecular basis of divergence between two populations with differing physiological responses. We present these novel findings: 1) acute low salinity conditions caused more deaths than high salinity, 2) molecular processes that elevate proline levels increased in 7ppt, which contrasts with other T. californicus studies that mainly associated accumulation of proline with hyperosmotic stress. We also find that 3) tolerance to a salinity fluctuation did not follow a latitudinal trend, but was instead governed by a complex interplay of factors including population and the duration of salinity stress. This highlights the importance of including a wider variety of environmental conditions in empirical studies to understand local adaptation. Overall design: 1. Population AB at 35ppt control, 2. AB at 7ppt, 3. AB at 35ppt recovery, 4. Population SD at 35ppt control, 5. SD at 7ppt, 6. SD at 35ppt recovery. There were 2 replicates for each number, totalling 12 Samples (libraries)