Trough ponds are ubiquitous features of Arctic landscapes and an important component of freshwater aquatic ecosystems. Permafrost thaw causes ground subsidence, creating depressions that gather water, creating ponds. Permafrost thaw also releases solutes and nutrients, which may fertilize these newly formed ponds. We measured water budget elements and chloride, ammonium, and dissolved organic nitrogen (DON) across a chronosequence of trough ponds representing different stages of ice wedge degradation and stabilization. We developed a coupled hydrologic and biogeochemical model to explore how ice wedge degradation affects hydrology and nutrient availability in trough ponds in the advanced degradation stages (DAs), which are characterized by deep troughs with warmer temperatures relative to the other stages. DAs experienced greater evaporation than the other stages, and subsurface inflows entered the DAs from a wide area. Chloride accumulated in the ponds with time since thaw, implying that subsurface fluxes are delivering solutes from the thawing permafrost. Ammonium accumulated at high rates in the initial degradation stage and was seasonally depleted over the summer in all degradation stages. Ammonium trends in the DAs were consistent with high concentration inflows and in‐pond assimilation at rates between 0.37 and 2.0 mg N m⁻² day⁻¹. Seasonal DON trends indicated that the accumulation of recalcitrant organic matter may eventually limit aquatic ecosystem production and foster pond infilling. These results provide direct evidence of nutrient release from thawing permafrost and the utilization of these nutrients by Arctic trough pond ecosystems and highlight infilling as a mechanism by which Arctic surface waters may be lost