Riverine input of dissolved nutrients (phosphorus and nitrogen) to the NW Black Sea shelf plays the main part in the marine water eutrophication. Between the rivers’ fresh water and open sea’s saline water, transient estuarine systems may be partial consumer or producer of nutrients. To obtain mean multiannual estimates of nutrients transport and metabolism in the largest estuarine system of Dnipro and South Bug rivers (Dnipro-Bug liman, DBL), regular observational data of 1992-2018 were collected and widely known LOICZ biogeochemical modelling approach and software were applied. Box model of water and substances transport was constructed consisted of two connected one-layer boxes. Each box has the entrance from the river and exits: from the first box – to the second one, and from the second box – to the adjacent sea. Using this model, the flows of water, salts and nutrients (dissolved inorganic phosphorus and nitrogen, DIP and DIN) were calculated. Non-conservative substance remnants, which are determined by internal biogeochemical (non-hydrographic) interactions were interpreted using Redfield’s relations. Fluxes of groundwater, precipitations and evaporation were found to be neglectable comparing to riverine input and water exchange fluxes. It was established that the nutrients outputs from the DBL to the sea are: 89,3 % of DIP and 41,4 % of DIN in relation to the total volume of these substances’ inflow to the DBL with river run-off. In general, in the DBL primary production outweighs the respiration, and denitrification significantly outweighs the nitrogen fixation. Numerical estimates of the DBL model correspond to the average long-term state. But it is available to analyze the response of the results on the input data variability by evaluating uncertainty using the Monte-Carlo (MK) method. According to MK-estimates, most variables of the DBL box model can vary on average in the range of only 19 – 25 % of their mean values, despite the large variability of nutrient inputs with riverine flows.