In this paper we describe the use of modified passive capillary samplers (PCSs) to investigate the water isotope variability of snowmelt at selected sites in Slovenia during winter 2011/2012 and during winter 2012/2013. First, PCS with 3 fibreglass wicks covering approximately 1 m2 were tested to determine sample variability. We observed high variability in the amount of snowmelt water collected by individual wick (185 to 345 g) and in the isotope composition of oxygen (δ18O −10.43‰ to −9.02‰) and hydrogen (δ2H −70.5‰ to −63.6‰) of the collected water. Following the initial tests, a more detailed investigation was performed in winter 2012/2013 and the variability of snowmelt on the local scale among the different levels (i.e. within group, between the close and more distant groups of wicks) was investigated by applying 30 fibreglass wicks making use of Analysis Of Variance (ANOVA) and a balanced hierarchical sampling design. The amount of snowmelt water collected by an individual wick during the whole experiment was between 116 and 1705 g, while the isotope composition varied from −16.32‰ to −12.86‰ for δ18O and from −120.2‰ to −82.5‰ for δ2H. The main source of variance (80%) stems from the variability within the group of wicks (e.g. within group) while other sources contribute less than 20% of the variability. Amount weighted samples for the 2012–2013 season show no significant differences among groups, but significant differences for particular sampling events were observed. These investigations show that due to the variability within the group of wicks, a large number of wicks (> 5) are needed to sample snowmelt.