The ongoing climate change affects the flow regime especially of small brooks and is probably related to more frequent extreme droughts, which impact populations of aquatic organisms. An example of strongly affected species is amphipod Gammarus fossarum that inhabits majority of small streams in the Czech Republic. We compared Gammarus populations from 5 pairs of permanent and intermittent sites with similar abiotic characteristics, to find out how were the population structures impacted by previous drought. The populations of gammarids were sampled in autumn after two months of recolonization, and the length of the head (from the upper edge of the head to the base of second antenna) was measured using the image analysis and later recalculated to body length. Intermittent sites had (i) lower after-drought abundance, (ii) predominance of males over females and (iii) fewer juveniles than permanent streams. Among each pair of sites (intermittent/permanent), there were also significant differences in the size structure of the populations. Smaller individuals were more abundant at permanent sites, while bigger individuals (mostly males) dominated at intermittent ones. Considering these results, we hypothesize that in studied streams permanent reaches (where adult specimens can survive drought) are more important sources for recolonization than small interstitial spaces (that are used mostly by juveniles). The differences in the structure of Gammarus fossarum populations at permanent and intermittent sites were noticeable even two months after reflooding, which indicate that used population characteristics have the potential for bioindication of the latest drought.