The modeling framework FlexSim is a fast, flexible and very user friendly tool specifically targeted towards scientific and management challenges of the complex biogeochemical processes in coastal zone ecosystems. FlexSim is a modular marine modeling framework, which contains a simplified formulation of estuarine hydrodynamics and more complex descriptions of pelagic and benthic biogeochemical processes. It has a very short computational time and can be easily adapted to different areas. FlexSim allows the user to set up computational grids of different complexity ranging from simple box model configurations to high-resolution unstructured grids. It can be applied by non-experts after a short introduction and might therefore be a good candidate to support managers and scientists without the need of an extensive computing infrastructure. Prototypes of FlexSim have been successfully tested for several Danish estuaries. Here, we present FlexSim and modeling results of the physical conditions in Horsens Fjord, an estuary on the east coast of Jutland, Denmark. Model simulations were carried out for different scenarios based on varying complexity of grid geometry and resolution. The model results were compared with observations from the Danish National Monitoring Programme.