The aim of this work is to simulate the dissolved oxygen deficiency in the coastal zone that sometimes occurs during the summer water stagnation. We consider the main components of the marine ecosystem that play a major role in such processes—concentrations of nitrogen, phosphorus and sulfur compounds in water, dissolved and particular organic matter, oxygen, biomass of phytoplankton and macroalgae. We use the object-based modeling technique to simulate the spatio-temporal variability of the ecosystem in a 2D domain. In comparison with the traditional approach, it gives several advantages: more precise parametrizations of the biological components’ functionality; higher spatial resolution; possibility to account for the individual variability of hydrobionts; easy inclusion of an arbitrary number of species in the model. Our model included three species of phytoplankton and seven macroalgae. Individual-based modules control their functionality. Species of phytoplankton and seaweeds chosen for simulations are typical for the coastal zone of Crimea. In the simulations, we study the contribution of micro- and macroalgae to the processes of self-purification of a semi-enclosed basin in case of a sharp increase in nutrient concentration in water.
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