The primary productivity of phytoplankton in Binh Cang - Nha Trang waters has been simulated by the 3D coupled ecological model. The model consists of an ecological module based on the interactions between 4 components (nutrient - phytoplankton - zooplankton and detritus) coupled to a nonlinear 3D baroclinic module in order to investigate the spatial and temporal distributions and dynamics of the primary productivity in Binh Cang - Nha Trang waters. The both modules'are driven by surface forcing at temporal level of 6h using reanalysis data of atmosphere from NCEP during 2008-2009, including: wind speed and direction, air temperatllre, relative humidity, cloudiness, rainfall and radiant flux. Data of temperature, salinity, nutrient, biology,... using for the model have been collected from published documents with high reliability as: the results of cooperative projects (Vietnam - Germany, Vietnam - Russia, Hab Viet), database (VODC) and website (http://pacificinfo.ru),...The simulated results for 2009 show that, the primary productivity in Binh Cang - Nha Trang waters have strongly varied according to the space and time and have been relative reasonable to observed results.