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Data from this study originate from the NSF (National Science Foundation) Polaris Project. The Polaris Project integrates scientific research in the Arctic-boreal region with education and outreach, with a primary focus on engaging and inspiring the next generation of scientists. The overarching scientific issue that drives the Polaris Project is the vulnerability and fate of ancient carbon stored in perennially frozen ground, permafrost. Although extensive permafrost thaw is expected to occur across the northern permafrost region this century, large uncertainties remain in the timing, magnitude, and form of carbon that will be released. Participants of the Polaris Project conducted field research in the Yukon-Kuskokwim Delta (YKD), collaborating to make fundamental scientific discoveries related to the transformation and fate of thawed permafrost carbon, and implications for global climate. This data set includes aquatic chemistry data from expeditions to the YKD during 2015–2019. Parameters measured include water temperature, pH, dissolved oxygen, conductivity, dissolved organic and inorganic carbon, nitrogen species, phosphorous, greenhouse gases, stables isotopes of carbon and water, optical properties of water, and fluxes of methane and carbon dioxide made in the field. These data were compiled and underwent quality assurance / quality control specifically for the scientific objectives of the manuscript published by Zolkos et al. (2022). Consequently, this dataset contains a modified version of Polaris Project YKD aquatic chemistry data previously published for 2015–2016 (http://doi.org/10.18739/A22804Z8M) and 2017 (http://doi.org/10.18739/A23775V7T). Data from 2018–2019 were not previously published. Therefore, users interested in the original datasets for 2015–2017 are encouraged to access them via the provided links, while users interested in the data and metadata specific to the associated manuscript by Zolkos et al. are encouraged to use this companion dataset.