We applied the FlexSem model framework for setting up a 3D coupled hydrodynamic-biogeochemical-sediment model for the Limfjorden (Larsen et al. 2020). The model framework was previously applied to study the impacts of intensified mussel farming (Maar et al. 2023a), mussel transplantation to mitigate hypoxia (Maar et al. 2021), mussel dredging (Pastor et al. 2020), dispersal of mussel larvae (Pastor et al. 2021), and drivers of hypoxia (Schourup-Kristensen et al. 2023) in the Limfjorden. The model used an unstructured mesh with 6686 elements with a total area of 1502 km2. The area of the elements varied from 20,368 m2 (length= 143 m) to 314,297 m2 (length= 1773 m) with an average of 224,579 m2 (length =474 m). The vertical resolution was 1.5 m in the flexible surface layer followed by nine 1 m depth layers, and three 5 m layers, with a maximum water depth of 30 m. The pelagic biogeochemical model in FlexSem was two-way coupled to a sediment biogeochemical model and a Dynamic Energy Budget (DEB)-population model (Maar et al. 2023a). The pelagic model simulated the cycling of nitrogen (N) and phosphorous (P) using Redfield ratios (Maar et al. 2011, Maar et al. 2016, Maar et al. 2022). The 11 state variables described concentrations of inorganic nutrients (NO3, NH4, PO4), PO4 adsorbed by metals in particles (PO4-metal), three functional groups of phytoplankton (diatoms, flagellates, picoplankton), micro- and mesozooplankton, detritus, and oxygen (Figure A1). The model considered the processes of nutrient uptake, growth, grazing, respiration, recycling, mortality, and settling of detritus and diatoms. Chl a concentrations were used as a proxy for phytoplankton biomass using a conversion factor of 2 mg Chl a (mmol-N)-1 (Thomas et al. 1992). The sediment model comprised an unconsolidated layer (Redfield ratios) exposed to resuspension, a consolidated layer with variable CNP-ratios, settled diatoms and mussel pellets, pore-water inorganic nutrients (NO3, NH4, PO4, and PO4-metal), deposit feeders, microphytobenthos, and oxygen. The DEB model described mussel growth as a function of temperature, salinity, and food levels and was previously parameterized and validated for the Limfjorden and the Baltic Sea (Buer et al. 2020, Taylor et al. 2021). The DEB model was coupled with the population model describing the abundance of mussels in the farms over time which was set to decrease exponentially over time due to self-thinning (Nielsen et al. 2016).