The park occupies a large plain, which was formed when a depression in Paleozoiccrystalline rocks was filled with organic and inorganic sediments, thus creating a sedimentary basin. The uppermost sediment levels are of fluvial and aeolian origin. The eastern parts of the park are dominated by silts and clays, creating less permeable soils, while the western parts contain soils that are coarser and more porous. There are faults that were generated during formation of the Andes, lying parallel to the Paraguay River. While the park's territory is gently sloping down from west to east, there is very little variety in elevation. The subtle differences become important in times of heavy rains and floods, when the area becomes inundated with pools of water connected by channels forming in the most low-lying areas.
Hydrography
The Pilcomayo River, after which the park is named, is the main watercourse of the area. During the wet season, the river and its tributaries flood the nearby areas, creating large swaths of interconnected lakes and marshes, most of which are temporary. The southern end of the park contains a larger lake called Laguna Blanca, which is a habitat for many waterfowl species and a resting point for migratory bird species coming from the Northern Hemisphere.
Climate
The park is located in a subtropical zone with annual mean temperature of and annual mean precipitation of. Summer temperatures can exceed, but during winters, frost is not uncommon. Winters are dry, while precipitation peaks in March and November. The area is affected by frequent tornadoes.
Flora
For the purposes of classifying the park's types of plants, the area can be divided into 4 distinct zones. One is savanna, which is dominated by the Caranday wax palm, an unofficial emblem of the area, towering over a dense cover of herbaceous plants. Other trees include such species as Acacia caven and Prosopis nigra. Wetlands are dominated by aquatic vegetation. Floating plants include water hyacinths, Limnocharitaceae, Nymphoides and Ludwigia. Another distinct zone is adjacent to the Pilcomayo River and its former channels, which are frequently flooded. It is dominated by riparian vegetation. Figs and sweetwood trees can be found there, covered by many species of lianas, vines and epiphytes. The patchy vegetation of the higher lands, forming distinctive "mountain islands", represent the fourth zone. Quebracho trees can frequently be found there.