In this study, an NPZD model and a trophic network model that contains organism groups on the higher trophic levels were developed and linked using the “bottom-up control” approach. Such a linkage of models provides the possibility to use the advantages of both models; reproducing of the erratic behaviour of nutrients and plankton as realistic as possible, while still taking the more complex organisms in the trophic network, which respond to external forcing in a larger time scale. The models developed in this study were applied to the Curonian Lagoon that is an important estuarine ecosystem for Lithuania. The tests and simulations have proven that the results of the NPZD model were accurate enough for representing the nutrient and phytoplankton dynamics in the Curonian Lagoon as well as spatial differences which are of ecological interest. Linkage with trophic network model demonstrated NPZD model results to be consistent with the Curonian Lagoons ecosystem. The modelling results showed that primary production is relatively high in the Curonian Lagoon and is unlikely to be controlled by the organisms that are on the higher trophic levels of the food web. Analysis of the NPZD model scenarios with different nutrients inputs revealed that phosphorus is the main limiting nutrient for primary production in the Curonian Lagoon. However, different combinations of nitrogen and phosphorus inputs control the relative abundance of different phytoplankton groups. Investigation of reaction of ecosystem to water temperature increase showed that the temperature increase finally leads to decrease of available phytoplankton to upper levels of the food web.