The Jacuí empties into the Guaíba River, an estuarine arm of the Lagoa dos Patos, a large coastal lagoon connected to the Atlantic Ocean.

At Porto Alegre, near the Atlantic coast, the Jacuí transforms into a shallow estuary, known as the Guaíba River, and flows into the Patos Lagoon.

The Dona Francisca Hydroelectric Dam impounds the upper Jacuí River, and is divided between the municipalities of Agudo and Nova Palma, Rio Grande do Sul.

[3] The Quarta Colônia State Park is on the left bank of the reservoir of the Dona Francisca dam, with an area of 1,847.9 hectares (4,566 acres).

[4] The estuary contains the Banhados do Delta Biological Reserve, which protects the islands of Pólvora and Pombas.