1. Natural and anthropogenic disturbances are influential factors in river ecosystems. Lowland rivers that cross urbanised areas experience direct disturbance due to urbanisation, affecting suitability for many vertebrate and invertebrate species and with important implications for ecosystem functioning and stability. In addition, lowland rivers are potentially subjected to major flood events, whose effects may be exacerbated by urbanisation in the river basin. A greater understanding of the combined effects of flood disturbance and urbanisation is needed if we are to preserve riverine ecosystems and improve management strategies. 2. We characterised macroinvertebrate, detritus-based food webs upstream and downstream of Rome (Italy) before a period of exceptional flooding and at intervals until 71 days following the final flood event. We studied community and food-web characteristics, combining carbon and nitrogen stable isotope analysis with macroinvertebrate population census data. 3. The flood altered the species assemblage at both upstream and downstream locations. The food webs shifted towards a more complex configuration, with increased trophic generalism, linkage density and mean chain length. However, the food web at the upstream location gradually recovered its pre-flood configuration, whereas at the downstream location, where flood effects were stronger, the food web showed little capacity for recovery within the time span of the study. The contrasting food-web responses can be explained with reference to differences in resource availability for detritivores and predators and in water turbidity, which in turn reflect an interaction between flood disturbance and river basin urbanisation. 4. The description of short-term variations in food-web properties may help to improve ecosystem monitoring and the management of freshwater bodies and can be used to assess short-term and long-term effects of disturbance. A better understanding of the negative effects of urban pressure on macroinvertebrate community stability should help to define appropriate measures for the conservation and restoration of urbanised river areas, especially given that extreme flood events are expected to increase due to climatic change