This work assesses the effectiveness of sample preservation techniques for measurements of pH_T (total scale), total dissolved inorganic carbon (C_T), and total alkalinity (A_T) in organic-rich estuarine waters as well as the internal consistency of measurements and calculations (e.g., A_T, pH_T, and C_T) in these waters. Using mercuric chloride (HgCl₂)-treated and untreated water samples, measurements of these carbonate system parameters were examined over a period of 3 months. Respiration of dissolved organic matter in untreated samples created large discrepancies in C_T concentrations (~37 μmol kg⁻¹ increase, p < 0.0001), while C_T was effectively constant in treated samples (3095.0 ± 1.14 μmol kg⁻¹). A_T changes were observed for both treated and untreated samples, with HgCl₂-treated samples showing the greatest variation (~ 26 μmol kg⁻¹ decrease, p < 0.001). In response to changing A_T/C_T ratios, pH_T changes occurred in both treated and untreated samples but were relatively small in treated samples. Results in organic-rich estuarine waters that reflect the in situ carbonate system characteristics of the samples at the time of collection can be improved when samples obtained for C_T and A_T analysis are collected and stored separately. Accurate analyses of C_T can be obtained by filtration and preservation with HgCl₂. Accuracy of A_T analyses can be improved by filtration and storage without adding HgCl₂. The quality of pH_T measurements can be improved by prompt analysis in the field and, if this cannot be accomplished, then samples can be preserved with HgCl₂ and measured in the laboratory within 1 week.