Despite an increasing focus on low level methods for determination of mercury species in water over the last decades, few studies have paid attention to direct effects of different sample preparation methods (i.e. preservation techniques) on natural freshwater samples. In this study we show how different preservation techniques give significantly different concentrations of total and methylmercury in freshwaters (9 and 14% on average, respectively). Natural stream samples from a forested lake catchment were studied. Mean stream sample concentrations of total (3.6 ng/L) and methylmercury (0.06 ng/L) reflect levels typical for pristine humic boreal catchments. The main reason for the observed average differences in total and methylmercury concentrations is the use of one instead of two sample bottles and timing of sample acidification, respectively.