The biogeochemical model in the FlexSem framework was based on a modification of the ERGOM model that originally was applied to the Baltic Sea and the North Sea. In the Disko Bay version, 11 state variables describe concentrations of four dissolved nutrients (NO3, NH4, PO4, SiO2), two functional groups of phytoplankton (diatoms, flagellates), micro- and mesozooplankton, detritus (NP), detritus-silicon, and oxygen. Further, pelagic detrital silicon was added to better describe the cycling and settling of Si in deep waters. The model currency is N using Redfield ratios to convert to P and Si. Chlorophyll a (Chl a) was estimated as the sum of the two phytoplankton groups multiplied by a factor of 1.7 mg-Chl/mmol-N. The calanoid copepod C. finmarchicus generally dominates the mesozooplankton biomass and the physiological processes were parameterized according to previous studies. The model considers the processes of nutrient uptake, growth, grazing, egestion, respiration, recycling, mortality, particle sinking and seasonal mesozooplankton migration in the water column and overwintering in bottom waters. NPP was estimated as daily means of phytoplankton growth after subtracting respiration and integrated over 30 m depth corresponding to the productive layer. Light attenuation (kd) is a function of background attenuation (water turbidity) and concentrations of detritus and Chl a. The new version was updated with a new second-order advection-diffusion scheme and new wind stress formulation.