The physiology of ion regulation in the highly invasive European green crab Carcinus maenas has been widely studied, but mostly in constant salinity conditions, and not in context of their molt cycle-dependent sternite coloration. The ventral sternites are typically green after molting, and turn red through prolonged intermolt, with a concurrent decrease in stress tolerance. In this study, whole animal and molecular physiology was evaluated at constant low salinity (12), and oscillating salinity (12–32 every 6 h). Performance in three whole animal measures revealed that the green phase is more tolerant than the red phase, and that females are more tolerant than the respective males under both salinity conditions. These differences result from larger increases in expression of the drivers behind ion transport (Na /K -ATPase, cytoplasmic carbonic anhydrase) in green phase and female crabs. Low salinity exposure resulted in increased expression of these markers compared with oscillating salinity, demonstrating that low salinity is more strenuous, as more cellular regulation is required. This agrees with the crabs' natural environmental conditions where prolonged low salinity is rarely experienced. These findings are presented in context of a crab population survey conducted from May 2012 through November 2016 in southern Maine, USA. Female and red phase crabs were found at higher proportions in the intertidal than previously reported. In addition, gravid females were found year round, which is indicative of continuous reproduction. The data demonstrate the necessity to evaluate C. maenas in an ecologically relevant context with respect to color phase within each invasive population to truly understand the invasive capabilities of this species and to better inform management strategies.