Nutrient concentration in the water of sea mouths of rivers is a limiting factor in the life activity of hydrobionts. Therefore, studying this parameter is important for assessing the current state of mouth ecosystems and its forecasting. Until now, the variability of nutrients has been analysed by their average concentrations over heterogeneous or short-term periods, extremes or individual surveys, which do not reflect the regime of these elements in the modern climatic period. The paper aims to give a modern description of the nutrient concentration variability in the Chernaya River estuarine zone and to assess water quality based on these components of the ecosystem. For the analysis, we used data from hydrochemical surveys for 1991-2020. Water quality was assessed by the nutrient water pollution index, whereas self-purifying capacity of the estuarine zone was assessed using a transformation index of selected nutrients. The distributions of nutrient concentrations were found to be extremely asymmetrical. In this regard, we obtained for the first time the distributions of medians of nitrates, nitrites, ammonium nitrogen and phosphates in the water of the Chernaya River estuarine zone. In the study area, these median concentrations of nutrients did not exceed the maximum permissible values. Analysis of the temporal variability of average annual nutrient concentrations showed the absence of significant trends. The obtained results can be used for balance estimates and calculations of the assimilation capacity of the Chernaya River estuarine zone.