—One of the most urgent problems on which current studies of Arctic and subarctic territories are focused is how permafrost thawing can affect organic carbon fluxes and how these fluxes can influence the geochemistry of the surface and ground water. In addition to disturbing the carbon balance, permafrost thawing provokes the release of a significant amount of other chemical elements entering natural waters. The paper presents original data obtained by studying surface water in 2020 in the Yamalo–Nenets Autonomous District, which is situated in the Arctic zone of the Russian Federation. Permafrost is widespread in the study area, as also are facilities of the oil and gas industry. This predetermines the importance of research on the chemical composition of natural water, its formation, and ecological–geochemical status, which are critical aspects for assessing the anthropogenic load and predicting the influence of climate changes on the biogeochemical cycles of chemical elements. In the course of our fieldwork, 47 surface water samples were taken in the basins of the Taz, Pur, Ob, and Nadym rivers: 23 samples from rivers and streams and 24 samples from lakes and thaw depressions. The sampling sites were chosen to as comprehensively as possible cover the lake–stream–river system in the catchment areas of major rivers of the Yamalo–Nenets Autonomous District. The chemical composition of the water samples was analyzed at a certified laboratory using methods conventionally applied in solving such problems. The data were processed using statistical methods, including the principal component analysis (PCA). Data analysis demonstrates that surface water in the study area is ultrafresh, with neutral or weakly alkaline pH values. Hydrocarbonate, calcium, and magnesium ions dominate in the ionic composition of the water, and ammonium contents are high in the waters of the lakes and thaw depressions. In addition, the ammonium concentration strongly positively correlates with the content of dissolved organic carbon (DOC) and the values of chemical oxygen demand (COD) and permanganate index (PI). It was found out that the streams (springs and rivers) differ from the lakes and the water of the thaw depressions in higher concentrations of main ions that are brought to the water mainly by natural factors (these are {text{HC}}{{{text{O}}}_{{text{3}}}}^{ - }, Ca2+, Mg2+, and Na+) and higher total dissolved solids (TDS) and pH values. In contrast, the water of the thaw depressions is characterized by the highest concentrations of DOC and the values of other parameters related to organic matter (N–{text{N}}{{{text{H}}}_{4}}^{ + }, COD, and PI). It was shown that the main factors that control the chemical composition of the water are its interaction with organic matter from organic (peat) soil horizons and the mineral components of the underlying rocks and soils. The former factor most significantly impacts the water of the thaw depressions, and the latter one affects mainly the chemical composition of the rivers and streams. The relatively high contents of the chloride and sodium ions in the water of the largest lakes are probably caused by the anthropogenic load.