A one-dimensional ecological model of the meromictic brackish Lake Shira (Russia, Khakasia) was developed. The model incorporates state-of-the-art knowledge about the functioning of the lake ecosystem using the most recent field observations and ideas from PCLake, a general ecosystem model of shallow freshwater lakes. The model of Lake Shira presented here takes into account the vertical dynamics of biomasses of the main species of algae, zooplankton and microbial community, as well as the dynamics of oxygen, detritus, nutrients and hydrogen sulphide from spring to autumn. Solar radiation, temperature and diffusion are modelled using real meteorological data. The parameters of the model were calibrated to the field data, after applying different methods of sensitivity analysis to the model. The resulting patterns of phytoplankton and nutrients dynamics show a good qualitative and quantitative agreement with the field observations during the whole summer season. Results are less satisfactory with respect to the vertical distribution of zooplankton biomass. We hypothesize that this is due to the fact that the current model does not take the sex and age structure of zooplankton into account. The dynamics of oxygen, hydrogen sulphide and the modelled positions of the chemocline and thermocline are again in good agreement with field data. This resemblance confirms the validity of the approach we took in the model regarding the main physical, chemical and ecological processes. This general model opens the way for checking various hypotheses on the functioning of the Lake Shira ecosystem in future investigations and for analysing options for management of this economically important lake.