An annual and a seasonal biogeochemical climatology had been constructed for the Southern Benguela Upwelling System, from <i>in situ</i> data collected along a 12 station monitoring line, sampled at monthly intervals from 2001 to 2012. The monitoring line reaches a maximum offshore distance of almost 190 km, with monitoring station depths ranging from 27 to 1465 m. In addition to temperature, salinity and oxygen CTD profile data, archived monitoring data for the macro-nutrients (phosphate, nitrate + nitrite, silicate) and chlorophyll-a was evaluated. The climatologies exhibit clear spatial and seasonal variability patterns for all parameters, that yield important insight into the SBUS upwelling cycle. These data sets comprise valuable additions to our knowledge base, and will aid both future modelling efforts and studies of biogeochemical processes in upwelling systems. Data for the constructed climatologies have been made available via the PANGAEA Data Archiving and Publication database at <a href="http://doi.pangaea.de/10.1594/PANGAEA.882218"target="_blank">http://doi.pangaea.de/10.1594/PANGAEA.882218</a>.