Summary1. To study the bottom-up linkages in arctic lakes, we treated one side of a partitioned lake with inorganic nitrogen and phosphorus for a 6-week period each summer for 6 years starting in the summer of 1985. We took a variety of weekly measurements to determine the impact of the nutrient loading on the lake and continued weekly measurements for 2–6 years after the cessation of nutrient loading to observe the recovery of the treated side. The loading rates (2.91 mmol N m−2 day−1 and 0.23 mmol P m−2 day−1) were five times the calculated loading rates for Toolik Lake, located nearby.2. In all 6 years of nutrient addition, phytoplankton biomass and productivity were greater in the treated sector than the reference sector. In the first 4 years of nutrient addition there was no flux of phosphorus from the mineral-rich sediments. This changed in the last 2 years of nutrient addition as phosphorus was released to the lake.3. The response of the animal community to increased plant production was mixed. One of the four macro-zooplankton species (Daphnia longiremis) increased in number by about twofold in the first 5 years. However, the copepod Cyclops scutifer showed no response during the treatment phase of the study. The benthic invertebrate response was also mixed. After a 2-year lag time the snail Lymnaea elodes increased in the treated lake sector but chironomids did not.4. Ecosystem response to fertilisation was not controlled solely by nutrient addition because phosphorus was not recycled from the sediments until the last 2 years of nutrient addition. Phytoplankton still showed the effects of nutrient addition in the recovery period and the hypolimnion of the treated sector was still anaerobic starting at 6 m in 1996.