The microbial control agent Bacillus thuringiensis var. israelensis (Bti) has been successfully used worldwide to reduce abundances of biting Nematocera (Diptera), often with little direct impact on non-target organisms observed. However, the potential for additional indirect effects on other ecosystem properties, including on trophic linkages within food webs, is poorly known. We investigated the effects of multiple-year mosquito control treatments using the Bti product VectoBac ® -G on the stable isotope composition of epigeal and soil-based consumers inhabiting replicate floodplains along the River Dalälven, Sweden. We observed significant changes in the isotopic composition of detritivores feeding at the base of floodplain food webs. Enchytraeid worms were characterised by 3.5% higher δ 13 C values in treated floodplains, suggesting increased consumption of δ 13 C-enriched food. The overall range of community-wide δ 15 N values was 56% greater in the treated floodplains, whilst δ 15 N values of oribatid mites were elevated by 97%. These results suggest extra fractionation in the transfer of nitrogen through floodplain food chains. We conjecture that the ecological mechanisms driving these food web shifts are (1) the mass mortality of high δ 13 C A. sticticus larvae, which leaves high concentrations of dead mosquito biomass deposited on soils at local scales, after the floodwaters have receded and (2) incorporation of the very high δ 13 C-enriched corn particles comprising the bulk of the VectoBac ® -G product into floodplain food webs. Our results suggest that repeated applications of Bti might have wider, still largely unknown implications for nutrient and energy cycles within floodplain ecosystems.