© 2015 Elsevier B.V. In preparing calcium carbonate samples for the measurement of various geochemical proxies, it is often necessary to remove contaminating phases while leaving the phase of interest altered as little as possible. Here we evaluate the effects of some common cleaning protocols (rinsing (H2O), bleach (~3% NaOCl), hydrogen peroxide (30%), sodium hydroxide (0.006-0.1M NaOH), and acid leaching (0.05N HNO3)) on the elemental (Li, B, Na, Mg, Sr, Ba, Pb, and U) and boron isotope composition of both biogenic and synthetic calcium carbonates formed in marine environments.In untreated samples, the presence of elevated concentrations of Na and Mg, the most abundant cations in seawater, can be reduced with minimal cleaning (e.g. rinsing). Cleaning protocols that cause partial dissolution are problematic, especially for samples that are compositionally heterogeneous because the remaining sample may be biased towards particular phases with distinctive elemental or isotopic compositions. We show that the use of either acid or unbuffered hydrogen peroxide can lead to partial dissolution which was associated with an increase in the U/Ca ratio of the remaining sample. Bleaching or rinsing with water did not result in significant sample dissolution, suggesting that these cleaning techniques may be safely used on heterogeneous samples. Cleaning treatments, other than those resulting in significant dissolution of heterogeneous samples, had no significant effect on δ11B, suggesting that boron isotopes are generally robust to the effects of sample pre-treatment.