We compared the effects of preservation and storage methods on total alkalinity (AT) of seawater, estuarine water, freshwater, and groundwater samples stored for 0-6 months. Water samples, untreated or treated with HgCl2, 0.45 µm filtration, or filtration plus HgCl2, were stored in polypropylene or borosilicate glass vials for 0, 1, or 6 months. Mean AT of samples treated with HgCl2 was reduced by as much as 49.1 µmol kg-1 (1.3%). Borosilicate glass elevated AT, possibly due to dissolving silicates. There was little change in AT of control and filtered samples stored in polypropylene, except for untreated groundwater (~ 4.1% reduction at 6 months). HgCl2 concentrations of 0.02-0.05% reduced the AT of fresh, estuarine, and ground water samples by as much as 35.5 µmol kg-1 after 1 month, but had little effect on the AT of seawater. Adding glucose as a carbon source for microbial growth resulted in no AT changes in 0.45 µm-filtered samples. We suggest water samples intended for AT analyses can be filtered to 0.45 µm, and stored in polypropylene vials at 4 °C for at least 6 months. Borosilicate glassware and HgCl2 can be avoided to prevent analytical uncertainties and reduce risks related to use of Hg2+.