CHN elemental analysis is a common and effective method for determining total carbon (TC), total organic carbon (TOC), inorganic carbon (IC) by difference, and total nitrogen (TN) in marine sediments. In this article, we identify and describe three problems related to CHN measurement in carbonate‐rich (>30% CaCO3) marine sediments and suggest mitigation methods to obtain the most accurate measurements of TC, TOC, IC, and TN. These problems involve (1) sample size limitations, (2) incomplete carbonate digestion during in‐situ acid addition, and (3) nitrogen contamination during acid additions. Carbonate‐rich marine sediments often have low TOC and TN content and are susceptible to incomplete combustion, due to their high IC (CaCO3) content, and require careful sample size selection to optimize analysis. Incomplete digestion of carbonate prior to TOC analysis can introduce significant error into the measurement, and here we propose a testing methodology to ensure effective carbonate digestion. Atmospheric contamination of sulfurous acid, used for carbonate digestion, is also observed and modeled, and we suggest steps to minimize this contamination. Overall, our results allow for the development of sediment‐specific protocols for accurate CHN measurements in carbonate‐rich marine sediments.