The Arctic is faced with rapid climatic changes, but in some areas, drastic changes in the abundance of herbivores represent an even greater agent of change. Increasing goose populations, especially midcontinent lesser snow geese (Chen caerulescens), have led to an extensive loss of vegetation in terrestrial habitats in the Arctic through heavy grazing and destructive foraging. Our aim was to evaluate the effect of geese on the freshwater systems in their Arctic breeding grounds. We sampled the water chemistry of lakes and ponds across a major goose breeding area in the Eastern Canadian Arctic and compared results to samples taken 13 years earlier to determine whether the changes in water chemistry, if evident, were consistent with effects of geese or of climate. Our results suggest that nutrient loadings have increased while most other parameters associated with the underlying geology and hydrology of the region have stayed in a similar range as a decade ago. The most significant changes were linked to nitrogen and phosphorus; phosphorus concentrations doubled between 2001/2002 and 2015, with the highest levels and greatest changes observed for wetlands inside versus outside of goose breeding areas. Our results suggest that geese are most strongly affecting nutrient loads in freshwaters inside breeding areas, which show evidence of ornithological eutrophication. Nutrient changes of this magnitude, especially in typically oligotrophic Arctic lakes, can have profound consequences on ecosystem structure and function and demonstrate how burgeoning waterfowl populations can act as a vector of rapid environmental change in Arctic freshwaters.