This dataset contains measurements of dissolved organic matter (DOM) composition and dissolved greenhouse gas concentrations (carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O)) collected from freshwater ecosystems in the Kytalyk Nature Reserve, northeastern Siberia, during the summer months of July–August 2016 and July 2017. Samples were obtained from a range of aquatic environments, including ponds, lakes, and fluvial systems, representing spatial variability across an Arctic tundra landscape underlain by continuous permafrost. The dataset includes dissolved organic carbon (DOC) concentrations, stable carbon isotope composition of DOC (δ¹³C-DOC), optical properties of chromophoric and fluorescent DOM derived from absorbance and excitation–emission matrix spectroscopy, and environmental parameters such as water temperature, pH, specific conductivity, and dissolved iron (Fe). Dissolved gas concentrations were determined using headspace equilibration followed by gas chromatography. Optical DOM indices include absorbance coefficients, spectral slopes, and fluorescence-based indices derived from parallel factor analysis. A subset of samples (n = 11) was analyzed using thermal desorption proton transfer reaction mass spectrometry to characterize DOM molecular composition. These data include bulk molecular metrics (e.g. hydrogen-to-carbon and oxygen-to-carbon ratios, average carbon number, and oxidative state of carbon) and relative contributions of compound classes such as aliphatics, aromatics, and highly unsaturated compounds. The data were collected to characterize DOM composition and dissolved greenhouse gas concentrations across different freshwater ecosystem types in an Arctic permafrost region and to support analyses of spatial variability in biogeochemical properties. The dataset provides a comprehensive set of physicochemical and spectroscopic measurements for use in studies of carbon and nitrogen cycling in Arctic freshwater systems.