Flooding results in short and long-term modifications of aquatic ecosystem structure and biodiversity. Cyclone Idai, which ravaged through Zimbabwe in 2019, had devastating consequences on aquatic ecosystems. However, the extent of habitat modification and consequent biodiversity shifts are unknown. This study focuses on the comparative analysis of (i) habitat structure and (ii) macroinvertebrate assemblages in headwater streams of the Odzi sub-catchment, Chimanimani District, Zimbabwe, specifically examining the conditions post-Cyclone Idai-induced flooding. Field sampling was conducted in the dry season (September−November) 2019 and wet season (January−March) 2020. Headwater streams of the Murare (first order), Umvumvumvu (first and second order) and Nyanyadzi (first and second order) rivers were sampled. Habitat assessment was done following the Benthic Macroinvertebrate Monitoring Protocol Implementation Plan. Selected water variables were measured using appropriate probes. Macroinvertebrate assemblage data were collected using the South African Scoring System (SASS 5) protocol. Spatiotemporal variations in water quality, habitat structure and macroinvertebrate metrics were assessed using two-way ANOVA, ANOSIM and SIMPER. Significant spatiotemporal heterogeneity (p < 0.05) was detected in temperature, turbidity, conductivity and total dissolved solids, velocity and depth regimes, channel flow status, sediment deposition, channel alteration and frequency of riffles for the three rivers. Habitat quality ascending hierarchical order was: Umvumvumvu > Murare > Nyanyadzi after Cyclone Idai induced flooding. The highest macroinvertebrate composition diversity was detected in Murare River, the least flood-affected stream. The largest dissimilarity (ANOSIM, 75.3%) was between the Umvumvumvu and Nyanyadzi rivers. Macroinvertebrate community structure differed significantly because of species uniqueness and heterogenous tolerance to changes in environmental conditions after flooding. Flooding intensity and duration induces dissimilar environmental tolerances and persistent macroinvertebrates communities in lotic systems across local catchment scales. Long-term assessment of water quality impairment, resilient functional feeder groups and rifflescale physical habitat structure are imperative for optimised micro-scale conservation of macroinvertebrates in headwater streams prone to flash flooding.