This research analyzed the effect of border vegetation and pastures on the physical-biotic structure in a border sector of an aquatic-terrestrial convergence area, of the San Francisco Marsh of the Ayapel Swamp System (ASS), through organism groups, such as aquatic and terrestrial vegetation, aquatic macroinvertebrates and periphyton. In general, during the first phase of the flood pulse, a greater abundance of aquatic vegetation and periphyton algae was found (18 genera were determined in the forest and 16 in the pasture). Additionally, three families of aquatic macroinvertebrates were found in each study area. Good quality water was also found in the forest area, while moderately polluted water was found in the pasture. In the second phase of the flood pulse, the nutrients increased, the aquatic vegetation and periphyton algae densities decreased (seven genera were found in the forest and eight in the pasture), whereas the aquatic macroinvertebrates density increased, identifying six families in the forest and four in the pasture. Finally, both study areas had moderately polluted water. It is important to conserve and recover the native vegetation because it allows the presence of periphyton organisms, and aquatic macroinvertebrates, thereby making possible inorganic carbon fixation, nutrients recycling and organic matter availability. These contribute to the fish recovery, which is a fundamental economic resource in Ayapel and the surrounding areas.