The phytoplankton primary production, pelagic respiration, photosynthetic pigments, and physical-chemical associated variables in the Pajarales Complex, were estimated to assess the potential effects of the Magdalena River recommunication with its former delta, The study carried out between September and December 2005, followed the same experimental design than one done before to the recommunication The results show a signicant increase of the net primary production when compared with the years 1988-89 (from 598 gC/m2/year to 982 gC/m2/year). The actual production seems to be driven mainly by ammonia, and there is no correlation neither with the water transparency nor the chlorophyll a concentration. The ecosystem is less efcient in the synthesis of organic matter after the recommunication with the Magdalena river. The respiration rate increased, showing higher and more prolonged heterotrophy, which may be associated to higher organic matter and inorganic nutrient inputs from the Magdalena River. The results conrm eutrophication increase in the CP between 1989 and 2005.