This research reports the simulation of ammoniacal nitrogen, nitrate orthophosphates and dissolved oxygen transport in the Ayapel wetland (Cordoba, Colombia), based on four sampling periods carried out between September 2004 and March 2005, for both rainy and dry seasons. The simulation was performed using the ELCOM and CAEDYM models (CWR, 2004); the first one simulates hydrodynamic conditions and the second one takes the results gotten by the first model to simulate the trophic chain. The calibration of biochemical parameters began establishing the most important phytoplanktonic species and biological parameters involved in the vegetative development of this species. Then, calibration of the chemical parameters to model the tracking of state variables in the wetland was developed trough the different processes in which they interact. Two control sites were used to calibrate the model with concentration profiles of the constituents under study. Other two sites which had complete information were used to validate the model. The results obtained for both scenarios showed coherently the field values. The obtained simulated results show good agreement with the field measurements.