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Most studies assessing the impacts of ocean acidification (OA) on benthic marine invertebrates have used stable mean pH/pCO2 levels to highlight variation in the physiological sensitivities in a range of taxa. However, many marine environments experience natural fluctuations in carbonate chemistry, and to date little attempt has been made to understand the effect of naturally fluctuating seawater pCO2 (pCO2sw) on the physiological capacity of organisms to maintain acid–base homeostasis. Here, for the first time, we exposed two species of sea urchin with different acid–base tolerances, Paracentrotus lividus and Arbacia lixula, to naturally fluctuating pCO2sw conditions at shallow water CO2 seep systems (Vulcano, Italy) and assessed their acid–base responses. Both sea urchin species experienced fluctuations in extracellular coelomic fluid pH, pCO2, and [HCO3−] (pHe, pCO2e, and [HCO3−]e, respectively) in line with fluctuations in pCO2sw. The less tolerant species, P. lividus, had the greatest capacity for [HCO3−]e buffering in response to acute pCO2sw fluctuations, but it also experienced greater extracellular hypercapnia and acidification and was thus unable to fully compensate for acid–base disturbances. Conversely, the more tolerant A. lixula relied on non-bicarbonate protein buffering and greater respiratory control. In the light of these findings, we discuss the possible energetic consequences of increased reliance on bicarbonate buffering activity in P. lividus compared with A. lixula and how these differing physiological responses to acute fluctuations in pCO2sw may be as important as chronic responses to mean changes in pCO2sw when considering how CO2 emissions will affect survival and success of marine organisms within naturally assembled systems.