A large body of evidence is documenting the impact of reduced pH on marine species and ecosystems. This information is used to infer the present and future impacts of ocean acidification. However, a vast majority of the studies were performed using constant pH and the high level of pH variability experienced by marine organisms on the coastal zone was often overlooked. Recent studies highlight the key role of this variability in driving biological response to pH as well as species sensitivity to ocean acidification. For example, it was hypothesized that because of local adaptation, the extreme of the present range of pH variability is a good predictor for local biological thresholds. Using a complex experimental design, we investigated what part of the pH variability is driving the biological response of the sea urchin Echinus esculentus larvae. Comparing stable (pH 8.13, 7.82, 7.53) and fluctuating treatments (12 h at pH 8.13 and 12 h at pH 7.53) following natural or inverted diurnal cycles, we were able to show that (i) under constant conditions, low pH deviating from the present range of natural variability had a negative effect on larval growth rate and calcification; (ii) under fluctuating conditions, a desynchronization of the pH variation with the photoperiod led to decreased larval growth rate and calcification; (iii) overall, larval fitness (survival, growth and calcification) was higher under fluctuating conditions as compared to constant. While these data do not support the hypothesis that the minimum pH is the main driver of the biological response, they provide evidence of adaptation to variability in a coastal species with associated a cost of plasticity but not a cost of canalization.