The Pacific geoduck clam is important in Native American culture, to ecosystems as biofilters and prey, and to the U.S. economy as a valuable fishery that provides revenue and jobs. To gain insight into how this species might fare with future ocean acidification, and if stress conditioning might be beneficial in aquaculture practices, we explored the effects of low static and variable pH exposure on juveniles and adults. We found that juveniles were able to overcome a developmental delay resulting from an initial low pH exposure, growing larger over time and when under a secondary low pH exposure. Genome characteristics and methylation variation supported these phenotypes, with altered DNA methylation occurring mainly within genes associated with specific biological processes. We found that adults experienced decreased survival and delayed reproductive development under static, but not variable low pH exposure. Offspring of adults exposed to variable low pH initially showed delayed larval development, but were able to compensate as juveniles and grew larger under variable low pH conditions while maintaining a lower, less variable metabolic rate. Taken together, stress exposure duration, intensity, and variation, and the developmental stage of the animal produce different phenotypes. These experiments show short-term rather than long-term and variable rather than static stress exposure give rise to beneficial phenotypes (e.g. less metabolic activity to achieve the same or greater size), and that DNA methylation is a mechanism by which these phenotypes can be expressed.