Increasing stream flow intermittence is one of the long-term effects of climate change in the Czech Republic. Episodes of stream drying can strongly affect the whole aquatic invertebrate communities and even change the population structure of some species. One of the amphipods, Gammarus fossarum, an inhabitant of small, often drying streams, widespread across the whole Czech Republic, lacks any drought-resistant stages and is therefore strongly affected by dry episodes. We studied changes in its population structure across 12 pairs of intermittent and perennial streams in years 2012-2016 and discovered, that populations from intermittent streams have a higher proportion of larger males and a lower proportion of juveniles in comparison to populations of perennial streams. This finding supports the hypothesis that a higher male recolonisation ability is related to bigger body size and therefore higher overall mobility. Comparison of fecundity in natural residual pools and nearby streams in 2017 also indicated a lower proportion of breeding females in natural residual pools, probably caused by an increase in predation in overcrowded residual pools or overall stress in this highly unstable habitat. That could lead to possible egg loss and restricted population recovery after stream inundation. Our study confirms that population structure of Gammarus fossarum is one of the possible indicators of previous dry episodes on small streams across the Czech Republic.