This dataset consists of biogeochemical parameters of nitrate, phosphate, oxygen, chlorophyll-a and phytoplankton concentrations, net primary productivity and attenuation generated by the POLCOMS-ERSEM coupled hydrodynamic-ecosystem model. The modelled dataset is from the Atlantic Margin Model (AMM) implementation, extending from 40.1 to 64.9 degrees latitude north and from 19.9 degrees longitude west to 13 degrees longitude east. The dataset is on a latitude/longitude grid with latitudinal resolution of 12.3 km and longitudinal resolution between 7.8 km and 14.2 km. The data are available as monthly averages saved in annual files for the 38 year period from January 1967 to December 2004. The dataset was generated by the Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) and the Plymouth Marine Laboratory European Regional Seas Ecosystem Model (ERSEM). This work is funded by the Natural Environment Research Council (NERC) National Capability funding in order to investigate the biogeochemical factors which affect primary production in the northwest European continental shelf. The dataset was generated by the UK National Oceanography Centre, Liverpool. The dataset consists of 38 data files in Climate and Forecast (CF) compliant NetCDF format. More information about the modelled data set and its applications can be found in Holt et al. (2012).