European directives (Water Framework Directive - WFD and Marine Strategy Framework Directive - MSFD) require a regular survey of several descriptors of the Environmental Status of coastal waters of the North-east Atlantic Ocean. Especially for the MSFD, which may concern large continental shelf areas where measurements are scarce, realistic ecological models can help assessing the Environmental Status. The ECO-MARS3D model of the pelagic ecosystem of the Bay of Biscay and English Channel continental shelf (NE Atlantic) has been developed for these applied purposes and validated against various types of historic data. This first paper deals with the basic biogeochemical version, which contains inorganic nutrients (NH4, NO3, PO4, Si(OH)4), three phytoplankton bulk types (diatoms, nanoflagellates and dinoflagellates), two zooplankton bulk types, particulate detrital forms and dissolved oxygen. A second paper presents a version of this model including 3 harmful phytoplanktonic groups. A simulation covering the 2000-2010 decade is compared to satellite sea surface data for temperature and surface chlorophyll, to the Southampton-Bilbao and Ouistreham-Portsmouth ferrybox surface data for temperature, salinity, chlorophyll and nutrients, to point samples provided by the French network of phytoplankton monitoring (REPHY) for inorganic nutrients and chlorophyll, and to high frequency time series of dissolved oxygen measured by a moored automatic buoy. From a spatial point of view, the model provides realistic fields of annual means of surface temperature (but with a systematic bias of about +1.0°C) and phytoplanktonic biomass. From a seasonal point of view, the temperature and salinity follow correctly the observed variations. For nutrient and total chlorophyll, the model succeeds in reproducing the difference amounting to one order of magnitude between the North Sea coastal zones and the oligotrophic oceanic zone above the abyssal plain of the bay of Biscay. It also reproduces the spring-neap tide oscillation visible in satellite observations of surface chlorophyll. Simulated seasonal cycles are realistic in the coastal stations, but the French Atlantic coast seems slightly too nutrient-rich. In coastal eutrophicated areas, the model does not produce chlorophyll peaks as high as measured. In the Vilaine bay (France), the summer hypoxic conditions (down to 4 mg/L O2 or less) are correctly reproduced. This ecological model has been used off-line to map some classical eutrophication descriptors (winter DIN and DIP, March-October 90th percentile of chlorophyll) used by the WFD and MSFD European directives. It has also been turned into an operational real-time mode, as part of the French Previmer project (now: http://marc.ifremer.fr/resultats/production_primaire).