The Rio Vargem do Braço, also known as the Rio Vargem do Cedro and Rio Pilões, originates within the Serra do Tabuleiro State Park in Santa Catarina, Brazil. This protected area covers 84,130 hectares and was established in 1975. The Serra do Tabuleiro reaches altitudes above 1,200 metres, making it the largest mountain formation in the east-central portion of the state, and the river descends from this heavily forested highland environment.

The river flows east-northeast from its headwaters before joining the Cubatão River near that river's mouth on the Atlantic Ocean, at a point known as Morro da Pipa. Geologically, the river's current course is relatively recent — evidence suggests it previously flowed north-northwest before a tectonic event redirected it to its present alignment.

The Rio Vargem do Braço serves as the primary water supply source for the greater Florianópolis metropolitan region, a function that carries significant implications for any paddling activity in terms of potential access restrictions and water management considerations. Paddlers should verify current regulations with local authorities before planning a trip, as water supply rivers in Brazil are often subject to use restrictions.

The surrounding landscape is characterized by the dense Atlantic Forest cover of the Serra do Tabuleiro State Park, one of the larger protected areas in Santa Catarina. The community of Vargem do Braço is located near the river's mouth, providing the closest point of human settlement along the lower reach of the river.