Description: Highlights • A new description of sediment phosphorus dynamics was implemented in a 3D-model. • Oxygen consumption affects oxygen penetration in coastal sediments. • Low oxygen concentrations determine the oxygen penetration in deeper water sediments. • More than 80% of the phosphorus loads (1980–2008) are retained in the Baltic Sea. • Phosphorus is released from anoxic sediments and retained in oxic sediments. Abstract The new approach to model the oxygen dependent phosphate release by implementing formulations of the oxygen penetration depths (OPD) and mineral bound inorganic phosphorus pools to the Swedish Coastal and Ocean Biogeochemical model (SCOBI) is described. The phosphorus dynamics and the oxygen concentrations in the Baltic proper sediment are studied during the period 1980–2008 using SCOBI coupled to the 3D-Rossby Centre Ocean model. Model data are compared to observations from monitoring stations and experiments. The impact from oxygen consumption on the determination of the OPD is found to be largest in the coastal zones where also the largest OPD are found. In the deep water the low oxygen concentrations mainly determine the OPD. Highest modelled release rate of phosphate from the sediment is about 59 × 103 t P year− 1 and is found on anoxic sediment at depths between 60–150 m, corresponding to 17% of the Baltic proper total area. The deposition of organic and inorganic phosphorus on sediments with oxic bottom water is larger than the release of phosphorus, about 43 × 103 t P year− 1. For anoxic bottoms the release of total phosphorus during the investigated period is larger than the deposition, about 19 × 103 t P year− 1. In total the net Baltic proper sediment sink is about 23.7 × 103 t P year− 1. The estimated phosphorus sink efficiency of the entire Baltic Sea is on average about 83% during the period.

Description: We present Nemo-Nordic, a Baltic and North Sea model based on the NEMO ocean engine. Surrounded by highly industrialized countries, the Baltic and North seas and their assets associated with shipping, fishing and tourism are vulnerable to anthropogenic pressure and climate change. Ocean models providing reliable forecasts and enabling climatic studies are important tools for the shipping infrastructure and to get a better understanding of the effects of climate change on the marine ecosystems. Nemo-Nordic is intended to be a tool for both short-term and long-term simulations and to be used for ocean forecasting as well as process and climatic studies. Here, the scientific and technical choices within Nemo-Nordic are introduced, and the reasons behind the design of the model and its domain and the inclusion of the two seas are explained. The model's ability to represent barotropic and baroclinic dynamics, as well as the vertical structure of the water column, is presented. Biases are shown and discussed. The short-term capabilities of the model are presented, especially its capabilities to represent sea level on an hourly timescale with a high degree of accuracy. We also show that the model can represent longer timescales, with a focus on the major Baltic inflows and the variability in deep-water salinity in the Baltic Sea.