The greatest discharges of the Paraguay River were studied using monthly series of Ladario, Brazil, at the outlet of the vast wetland of the Pantanal, and Asunción, Paraguay, at the middle Paraguay River outlet. Most of the major discharges at Asunción peaked between May and July, in phase with the annual maximum of the river discharges. They originated in the upper and middle Paraguay basins and were independent of the Pantanal output because their climate forcings were different from those of the Pantanal. In fact, most of the major discharge contributions from the upper and middle Paraguay basins occurred during El Niño (EN) periods, while at the Pantanal outlet they happened in neutral periods. The top discharge occurred during the autumn following the EN onset year. The composite of these cases has a tropospheric circulation that enhances the subtropical jet and the cyclonic vorticity advection over the Alto Paraná and the upper and middle Paraguay basins, favoring large positive anomalies in the precipitation field. Not all the major discharges were related to EN. Particularly, the major discharges that peaked in winter shared common features, despite their occurrence during EN, La Niña, or the neutral phases. Their April to August fields had an almost barotropic pattern at high latitudes with a deep cyclonic anomaly between 120Њ and 160ЊW and an anticyclonic anomaly over the southern tip of South America. This pattern is consistent with a northward shift of the synoptic perturbation tracks, which favors fields of positive precipitation anomalies over the Paraguay basin.