Northern high-latitude deltas are hotspots of biogeochemical processing, terrestrial-aquatic connectivity, and, in Alaska’s Yukon-Kuskokwim Delta (YKD), tundra wildfire. Yet, wildfire effects on aquatic biogeochemistry remain understudied in northern delta regions, thus limiting a more comprehensive understanding of high latitude biogeochemical cycles. In this study, we assess wildfire impacts on summertime aquatic biogeochemistry in YKD tundra using a multi-year (2015–2019) dataset of water chemistry measurements (n = 406) from five aquatic environments: peat plateau ponds, fen ponds, fen channels, lakes, and streams. We aimed to (i) characterize variation in hydrochemistry among aquatic environments; (ii) determine wildfire effects on hydrochemistry; and (iii) assess post-fire multi-year patterns in hydrochemistry in lakes (lower terrestrial-freshwater connectivity) and fen ponds (higher connectivity). Variation in hydrochemistry among environments was more strongly associated with watershed characteristics (e.g., terrestrial-aquatic connectivity) than wildfire. However, certain hydrochemical constituents showed consistent wildfire effects. Decreases in dissolved organic carbon (DOC) and CO2, and increases in pH, specific conductance, NH4+, and NO3– indicate that, by combusting soil organic matter, wildfire reduces organics available for hydrologic transport and microbial respiration, and mobilizes nitrogen into freshwaters. Multi-year post-fire variation in specific conductance, DOC, and CO2 in lakes and fen ponds suggest that watershed characteristics underlie ecosystem response and recovery to wildfire in the YKD. Together, these results indicate that increasing tundra wildfire occurrence at northern high latitudes could drive multi-year shifts toward stronger aquatic inorganic nutrient cycling, and that variation in terrain characteristics is likely to underlie wildfire effects on aquatic ecosystems across broader scales.