Chaoborus spp. (phantom midge) are prevalent in eutrophic inland waters. In Lake Soppen, Switzerland, C. flavicans larvae diurnally migrate between the methane-rich, oxygen-depleted hypolimnion and sediments, and the methane-poor, oxygen-rich epilimnion. Using a combination of experiments and system modelling, this study demonstrated that the larvae's burrowing activities in and out of the sediment perturbed the sediment and re-introduced sequestered phosphorus into the overlying water at a rate of 0.022 μg P ind−1 d−1, thereby exacerbating internal nutrient loading in the water column. Fluxes of sediment methane and other reduced solutes enhanced by the larval bioturbation would consume oxygen and sustain the hypoxic/anoxic condition below the thermocline. In addition to increasing diffusive fluxes, migrating larvae also directly transported methane in their gas vesicles from the deep water and release it in the surface water at a rate of 0.99 nmol CH4 ind−1 d−1, potentially contributing to methane emission to air. As nutrient pollution and climate warming persist or worsen in the coming decades, proliferation of Chaoborus could intensify this positive feedback loop and delay lake recovery.