The head of navigation is located in Brazil, and during most years vessels with 21 m drafts can reach Concepción without difficulty. Medium-sized ocean vessels can sometimes reach Asunción, but the twisting course and shifting sandbars can make this transit difficult. Although sluggish and shallow, the river sometimes overflows its low banks, forming temporary swamps and flooding villages. River islands, meander scars, and oxbow (U-shaped) lakes attest to frequent changes in course.
The major tributaries entering the Paraguay River from the Paraneña region - such as the Apa, Aquidabán, and Tebicuary Rivers - descend rapidly from their sources in the Paraná Plateau to the lower lands. There they broaden and become sluggish as they meander westward. After heavy rains these rivers sometimes flood nearby lowlands.
About 4700 km long, the Paraná River is the second major river in the country. From Salto del Guairá, where the river enters Paraguay, the Paraná River flows 800 km to its juncture with the Río Paraguay and then continues southward to the Río de la Plata Estuary at Buenos Aires, Argentina. In general, the Río Paraná is navigable by large ships only up to Encarnación, Paraguay but smaller boats may go somewhat farther. In summer months the river is deep enough to permit vessels with drafts of up to three meters to reach Salto del Guairá, but seasonal and other occasional conditions severely limit the river's navigational value. On the upper course, sudden floods may raise the water level by as much as five meters in twenty-four hours; west of Encarnación, however, the rocks of the riverbed sometimes come within one meter of the surface during winter and effectively sever communication between the upper river and Buenos Aires.
The rivers flowing eastward across the Paraneña region as tributaries of the Paraná River are shorter, faster-flowing, and narrower than the tributaries of the Paraguay River. Sixteen of these rivers and numerous smaller streams enter the Paraná River above Encarnación.
Paraguay's third largest river, the Pilcomayo River, flows into the Paraguay River near Asunción after demarcating the entire border between the Chaco region and Argentina. During most of its course, the river is sluggish and marshy, although small craft can navigate its lower reaches. When the Pilcomayo River overflows its low banks, it feeds the Patiño Estuary (Estero Patiño).
Drainage in the Chaco region is generally poor because of the flatness of the land and the small number of important streams. In many parts of the region, the water table is only a meter beneath the surface of the ground, and there are numerous small ponds and seasonal marshes. As a consequence of the poor drainage, most of the water is too salty for drinking or irrigation.
Because of the seasonal overflow of the numerous westward-flowing streams, the lowland areas of the Paraneña region also experience poor drainage conditions, particularly in the Ñeembucú Plain in the southwest, where an almost impervious clay subsurface prevents the absorption of excess surface water into the aquifer. About 30 percent of the Paraneña region is flooded from time to time, creating extensive areas of seasonal marshlands. Permanent bogs are found only near the largest geographic depressions, however.