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Abstract Permafrost thaw alters groundwater flow, river hydrology, stream‐catchment interactions, and the availability of carbon and nutrients in headwater streams. The impact of permafrost on watershed hydrology and biogeochemistry of headwater streams has been demonstrated, but there is little understanding of how permafrost influences fish in these ecosystems. We examined relations among permafrost characteristics, the resulting changes in water temperature, stream hydrology (e.g., discharge flashiness), and macroinvertebrates, with the abundance, biomass, and energy density of juvenile Dolly Varden (Salvelinus malma) and Arctic Grayling (Thymallus arcticus) across 10 headwater streams in northwestern Alaska. Macroinvertebrate density was driven by concentrations of dissolved carbon and nutrients supporting stream food webs. Dolly Varden abundance was primarily related to water temperature with fewer fish in warmer streams, whereas Dolly Varden energy density decreased with the flashiness of the headwater streams. Dolly Varden biomass was related to both temperature and bottom‐up food web effects. The energy density of Arctic Grayling decreased with warmer temperatures and discharge flashiness. These relations demonstrate the importance of terrestrial–aquatic connections in permafrost landscapes and indicate the complexity of landscape effects on fish. Because permafrost thaw is one of the most impactful changes occurring as the Arctic warms, an improved understanding of how stream temperature, hydrology, and bottom‐up food web processes influence fish populations can aid forecasting of future conditions across the Arctic. 

Abstract Fluxes of carbon dioxide (CO₂) and methane (CH₄) from open water bodies are critical components of carbon‐climate feedbacks in high latitudes. Processes governing the spatial and temporal variability of these aquatic greenhouse gas (GHG) fluxes are still highly uncertain due to limited observational data sets and lack of modeling studies incorporating comprehensive thermal and biochemical processes. This research investigates how slight variations in climate propagate through the biogeochemical cycles of ponds and resulting impacts on GHG emissions. We examine the thermal and biogeochemical dynamics of two ponds in the Yukon–Kuskokwim Delta, Alaska, under varying climatic conditions to study the impacts on CO₂, CH₄, and oxygen (O₂) concentrations and fluxes. We performed multiple numerical experiments, using the LAKE process‐based model and field measurements, to analyze how these ponds respond to variations in air temperature, shortwave radiation, and snow cover. Our study demonstrates that ice cover duration and water temperature are primary climatic drivers of GHG fluxes. Climate experiments led to reductions in ice cover duration and increased water temperatures, which subsequently enhanced CH₄and CO₂gas emissions from two study ponds. On average, cumulative CH₄and CO₂emissions were 5% and 10% higher, respectively, under increases in air temperature and shortwave radiation. Additionally, we uncovered a need to incorporate groundwater influxes of dissolved gases and nutrients in order to fully represent processes governing aquatic biochemical activity. Our work highlights the importance of understanding local‐scale processes in predicting future Arctic contributions to GHG emissions.