Floods are naturally occurring extreme hydrological events that affect stream habitats and biota at multiple extents. Benthic macroinvertebrates (BM) are widely used to assess ecological status in rivers, but their resistance and resilience to floods in medium-sized, temperate, lowland rivers in Europe have not been sufficiently studied. In this study, we quantified the effect of a moderate (5-year return period) yet long-lasting and unpredictable flood that occurred in summer 2020 on the BM community of the Jeziorka River in central Poland. To better understand the mechanisms by which the studied flood affected the BM community, we also evaluated the dynamics of hydrological, hydraulic, channel morphology, and water quality conditions across the studied 1300 m long reach. Continuous water level monitoring, stream depth surveying, and discharge measurements. As well, in-situ and lab-based water quality measurements were carried out between March and August 2020. BM communities were sampled three times at eight sites along the reach, once before and twice after the flood. High flow velocities during the flood resulted in stream bed instability leading to sand substrate movement that caused streambed aggradation by up to 0.2 m. Dissolved oxygen and ammonium-nitrogen were major drivers of BM community structure. Taxa richness, abundance, and the BMWP-PL index declined significantly, whereas Shannon evenness and Simpson diversity indices showed no significant change in the first post-flood sampling, as indicated by Kruskal–Wallis and Tukey tests. Non-metric multidimensional scaling (NMDS) analysis showed that community composition was also significantly affected by the flood. Seven weeks after the flood peak (August 2020 sampling), BM communities had fully recovered from the disturbance. The results can serve as a first approximation of the resistance and resilience of BM communities for relevant applications in other medium-sized, low-gradient, temperate rivers.