The increased absorption of atmospheric CO2 by the ocean affects carbonate chemistry and calcification rates of marine organisms. The impacts of low pH and seawater warming were investigated for the intertidal gastropods Nassarius nitidus and Columbella rustica. The combined effect of reduced pH (7.6) and increased temperature (25 °C) was studied at intermediate time intervals for a total period of 3 months in order to investigate variability and fluctuations of the shell structure and density over time. The pH and temperature conditions used for the experiment were selected according to the predictions of the Intergovernmental Panel on Climate Change. Deterioration of the external surface structure and reduction of shell density of the gastropods were confirmed using an innovative imaging and analysis method based on micro-computed tomography. The effect of low pH at ambient temperature was detrimental for N. nitidus with a 38.1% reduction of density in the shell lip and a 47.7% decrease in the apex, which is the oldest shell region. C. rustica was also affected, although to a much lesser degree (the maximum reduction observed was 8% at the apex). The negative effects of reduced pH were further reinforced for C. rustica when the temperature was increased, while N. nitidus was not affected significantly by the combination of the two factors. Increased temperature at ambient pH had an inhibitory effect on the shell density of N. nitidus causing a reduction of about 40%, whereas the shell density of the widest and lip regions of the C. rustica were increased under the same conditions. Different species are characterised by different vulnerability and tolerance responses regarding ocean acidification and warming, and this variability may affect ecological interactions and marine biodiversity.