In order to obtain quantitative estimates of water and nutrient fluxes into the Dniester estuary system, the biogeochemical modeling approach recommended by the international program LOICZ was used. The integral (reservoir) model of the system consists of balance equations for water, salinity and dissolved forms of nitrogen and phosphorus. The research involves the information of the annual cycle (from November 2003 to October 2004) of hydrochemical studies at the mouth of the Dniester River and at the exit of the estuary to the Black Sea carried out within the framework of the international project GEF/BSERP, as well as the data of hydrometeorological observations at Belgorod-Dniestrovsky hydrometeorological station, Tzargorod Gyrlo hydrometeorological post and Odesa State Environmental University training base.
 The water balance equation takes into account the flows of river runoff, precipitation and evaporation. Uncertainty associated with the failure of taking into account the underground runoff still remained. The use of an independent empirical assessment of the advective water flow through the Tzargorod Strait made it possible to estimate the degree of non-stationarity of the model equations on the scale of variability from a month to a year. The flow of turbulent exchange between the estuary and the adjacent sea is estimated by means of the salt balance equation and is determined by the difference between the estuary and marine water salinity.
 By calculating the monthly and yearly values it was established that, for the Dniester estuary and similar systems, the water balance equation can be considered as stationary while the precipitation and evaporation flows can be neglected: compared to the river runoff, advective and turbulent water exchange flows they are several orders of magnitude lower, that is, below the limit of errors of horizontal water flows.
 The joint action of the advective and diffusion flows ensured the overall removal of nutrients from the estuary ecosystem. During the annual cycle of 2003-2004 observations 73% of total dissolved phosphorus and 92% of total dissolved nitrogen entered the sea from the estuary compared to the amount reaching the estuary with the Dniester River runoff.
 Stoichiometric analysis of biogeochemical residuals showed that, for most of the year, the ecosystem of the Dniester estuary produced organic matter and consumed dissolved phosphorus, while the nitrogen fixation in the ecosystem outweighed the denitrification process.
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