Anthropogenic carbon perturbation has caused decreases in seawater pH and increases in global temperatures since the start of the 20th century. The subsequent lowering of the saturation state of CaCO3 may make the secretion of skeletons more problematic for marine calcifiers. As organisms that precipitate thin aragonite shells, thecosome pteropods have been identified as being particularly vulnerable to climate change effects. Coupled with their global distribution, this makes them ideal for use as sentinel organisms. Recent studies have highlighted shell dissolution as a potential indicator of ocean acidification; however, this metric is not applicable for monitoring pH changes in supersaturated basins. In this study, the novel approach of high resolution computed tomography (CT) scanning was used to produce quantitative 3-dimensional renderings pteropod shells to assess the potential of using this method to monitor small changes in shell biometrics that may be driven by climate change drivers. An ontogenetic analysis of the shells of Cavolinia inflexa and Styliola subula collected from the Mediterranean was used to identify suitable monitoring metrics. Modern samples were then compared to historical samples of the same species, collected during the Mediterranean leg of the Thor (1910) and Dana (1921) cruises to assess whether any empirical differences could be detected. Shell densities were calculated and scanning electron microscopy was used to compare the aragonite crystal morphology. pH for the collection years was hind-cast using temperature and salinity time series with atmospheric CO2 concentrations from ice core data. Historical samples of S. subula were thicker than S. subula shells of the same size from 2012 and C. inflexa shells collected in 1910 were significantly denser than those from 2012. These results provide a baseline for future work to develop monitoring techniques for climate change in the oceans using the novel approach of high-resolution CT scanning.