“…For this effort, we included 19 state variables: two species of phytoplankton (diatoms P1 and dinoflagellates P2), labile and refractory dissolved organic carbon and particulate organic carbon, NH 4 , nitrate (NO 2 + NO 3 ), labile and refractory dissolved organic nitrogen and particulate organic nitrogen, PO 4 , DO, DIC, and total alkalinity. The biogeochemical model includes new upgrades, a sediment diagenesis module that allows directly coupled interaction between the water column and sediments through the processes of organic sediment settling and burial and remineralization and carbonate chemistry with DIC, total alkalinity, p CO2, and pH (Bianucci et al, ; Pelletier et al, ). With the aid of improvements described above, observed biogeochemical cycles (i.e., salinity, temperature, DO, nitrate, algal biomass, and pH) in the Salish Sea, including near‐bed hypoxia in locations such as the Lynch Cove region of Hood Canal, have been reproduced.…”