A dramatic increase in the breeding population of geese has occurred over the past few decades at Svalbard. This may strongly impact the fragile ecosystems of the Arctic tundra because many of the ultra-oligotrophic freshwater systems experience enrichment from goose feces. We surveyed 21 shallow tundra ponds along a gradient of nutrient enrichment based on exposure to geese. Concentrations of total phosphorus (P) and dissolved inorganic nitrogen (DIN) in the tundra ponds ranged from 2–76 to 2–23 μg l−1 respectively, yet there was no significant increase in phytoplankton biomass (measured as chlorophyll a; range: 0.6–7.3 μg l−1) along the nutrient gradient. This lack of response may be the result of the trophic structure of these ecosystems, which consists of only a two-trophic level food chain with high biomasses of the efficient zooplankton grazer Daphnia in the absence of fish and scarcity of invertebrate predators. Our results indicate that this may cause a highly efficient grazing control of phytoplankton in all ponds, supported by the fact that large fractions of the nutrient pools were bound in zooplankton biomass. The median percentage of Daphnia–N and Daphnia–P content to particulate (sestonic) N and P was 338 and 3009%, respectively, which is extremely high compared to temperate lakes. Our data suggest that Daphnia in shallow arctic ponds is heavily subsidized by major inputs of energy from other food sources (bacteria, benthic biofilm), which may be crucial to the persistence of strong top–down control of pelagic algae by Daphnia.