Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Chemical Geology 398 (2015): 11-21, doi:10.1016/j.chemgeo.2015.01.019. ; 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 – 0.1 M NaOH), and acid leaching (0.05 N 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 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. ; Research conducted at the University of Western Australia was supported by the Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies. Research conducted at WHOI was supported by NSF grant OCE- 1338320. M.H. was supported by an ARC Super Science Fellowship (at UWA) and a NSF International Research Fellowship (at CSM). T.D. was supported by a NSF Graduate Research Fellowship. M.M. was supported by a Western Australian Premiers Fellowship and an ARC Laureate Fellowship. This study was financially supported in part by Strategic Young Researcher Overseas Visits Program for Accelerating Brain Circulation (G2301, the Japan Society of the Promotion of Science awarded to KT).