The 591-sq-km park is separated into two sectors of the high Andes along the international highway to Argentina via Paso de San Francisco. The larger Sector Laguna Santa Rosa comprises 470 sq km surrounding its namesake lake at 3700m, and includes the dirty-white salt-flat Salar de Maricunga to the north.

The considerably smaller Sector Laguna del Negro Francisco surrounds a lake of the same name. The shallow waters are ideal for the 8000 birds that summer here, including Andean flamingos, Chilean flamingos and few rare James flamingos. The highest quantity of birds is present from December through February.