Among aquatic ecosystems, estuarine lagoons are generally more complex than inland waters because of the combined effect of the land and the sea. These systems are under the influence of land through the rivers and have a restricted and temporally variable water exchange with the seas or the oceans. Estuarine lagoons are generally productive ecosystems which offer habitats for many species. Many coastal and estuarine lagoons are known to be important components of the natural capital providing opportunities for aquaculture. These ecosystems are difficult to analyze. Like most of the transitional waters, their trophic and ecological status cannot be defined easily because of their complexity. Most of them are usually under strong human influence or already modified heavily, which makes this task even more difficult. Nutrient Phytoplankton Zooplankton Detritus (NPZD) models can help scientists to analyze the full picture of an aquatic system, together with physical, chemical and biological processes, to fill in the gaps of data between samplings and to forecast environmental changes and use this output for planning. Traditionally, these models have been developed and used by engineers extensively, usually with the aim of water resources and quality management. However, different needs may arise in ecological studies with different aims such as better understanding how an aquatic ecosystem works or analyze the interactions in an aquatic food web. In this case, different state variables may be needed than the conventional ones, which are used by more general water quality models that are available. In ecological studies, related to coastal lagoon ecosystems organism groups on the higher trophic levels can be of interest. In this study, an NPZD model and a trophic network model that contains organism groups on the higher trophic levels were 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 behavior 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.