Small, permanent streams are at risk of becoming stagnant or intermittent because of hydrological changes induced by climate change, which can be further intensified by anthropogenic disruptions, such as water abstraction. Macroinvertebrate communities are vulnerable to such changes because they depend on stream hydromorphological regime. We conducted a fully controlled field experiment in 1 impacted and 1 unimpacted Danish lowland stream with contrasting nutrient availability. We used dams and diversions to create short-term (2–10 wk) stagnant and drought conditions, and we installed pools in the drought area to test their value as refugia for benthic macroinvertebrates. After 2 wk, community composition had changed significantly in all treatments in both streams. The abundance of Chironomidae increased and the abundance of mayflies (Baetis rhodani), stoneflies (Amphinemura standfussi, Leuctra nigra), caddisflies (Silo pallipes, Sericostoma personatum), the amphipod Gammarus pulex, and some Diptera taxa (Simuliidae, Dicranota sp.) decreased relative to the control. Diversity and total abundance did not change in the stagnant or drought treatments, so we do not consider these variables sensitive to effects of short-term flow reductions. Diversity decreased (unimpacted stream) or was not affected (impacted stream) in pools relative to the drought treatment. Thus, pools did not act as a substantial refugium for macroinvertebrates under extreme low-flow conditions. Current velocity and amount of deposited organic material explained most of the change in the macroinvertebrate community. Nutrient availability did not influence the response of the macroinvertebrate community to the treatments, probably because the physicochemical changes were exacerbated in the impacted stream and outweighed the expected higher resilience of this community. Our results clearly demonstrate that short-term stagnation and droughts in lowland streams can cause strong alteration of species composition.