Indirect impacts of climate change, mediated by new species interactions (including pathogens or parasites) will likely be key drivers of biodiversity reorganization. In addition, direct effects of extreme weather events remain understudied. Simultaneous investigation of the significance of ectoparasites on host populations and extreme weather events is lacking, especially in the Arctic. Here we document the consequences of recent black fly outbreaks and extreme precipitation events on the reproductive output of an arctic top predator, the peregrine falcon (Falco peregrinus tundrius) nesting at the northern range limit of ornithophilic black flies in Nunavut, Canada. Overall, black fly outbreaks and heavy rain reduced annual nestling survival by up to 30% and 50% respectively. High mortality caused by ectoparasites followed record-breaking spring snow precipitation, which likely increased stream discharge and nutrient runoff, two key parameters involved in growth and survival of black fly larvae. Using the RCP4.5 intermediate climate scenario run under the Canadian Global Climate Model, we anticipate a northward expansion of black fly distribution in Arctic regions. Our case study demonstrates that, in the context of climate change, extreme weather events can have substantial direct and indirect effects on reproductive output of an arctic top-predator population.