Compared to aquatic ecosystems in temperate zones, tropical flood plain lake systems are highly complex, and poorly understood. This work evaluated the variation of primary production and phytoplankton biomass in one station in Escobillitas swamp in the complex of Ayapel system, located in northern Colombia. Primary production presented variation in relation to the flood pulse, as it ranged from 0 (high water ascent in 2007) and 191.6 mgC m-2 d-1 (high water on the decline in 2007) with an average value of 108.6 mgC m-2 d-1. We found the highest gross primary production in high water falling, a condition accompanied by increased algal biomass photosynthetic efficiency, reduction low rates in respiration and the P / B and P / R. ratios. Between consecutive hydrological cycles variations in the patterns of primary production the high water rising in 2006 had a low biomass, high PPB, with the highest photosynthetic efficiency, and low respiration rates; in contrast, for the same period of the hydrological flood pulse in 2007, an increase in biomass and reducing of PPB, photosynthetic efficiency, P / B ratio and respiration were observed. The water system changed between euproductive and oligoproductive, which indicates a high trophic dynamics.