Temporary streams are becoming increasingly common, but ecological responses to streambed drying are poorly characterized in the temperate continental region of central Europe. In addition, global research has focused on community responses to drying, whereas effects on individual populations remain unknown. We explored the population structure of Gammarus fossarum (Crustacea: Amphipoda) in a central European temporary stream. Benthic gammarids were sampled on five dates during a flow recession, one date between two drying events (of 10 and 20 days, respectively), and five dates after flow resumed. Additional benthic samples were taken from isolated pools and dry sediments during drying events, and freeze cores were collected to compare the vertical distribution of amphipods during wet and dry phases. Gammarids were measured, adults distinguished from juveniles, adults sexed, and female reproductive state determined. Densities increased during flow recession, potentially reflecting both a decline in submerged habitat availability and seasonal increases in juvenile abundance. Persistence within dry benthic sediments was minimal, whereas pools and saturated subsurface sediments supported high population densities. Juveniles comprised 80% of the subsurface population, suggesting that their ability to inhabit small interstices promotes persistence within the dry reach. Juveniles also comprised 92% of pool inhabitants, despite their potential exposure to predation. Adults dominated after flow resumed, and population structure was altered post-drying by the loss of spring-recruited juveniles and reproductive females. Our results suggest that streambed drying may have longer-term effects than typically characterized by community-level studies. We recommend management actions that support populations of ecologically important species as they adapt to changing flow regimes.