It forms within the Cordillera Central mountain range southwest of the city of Bonao in Monseñor Nouel Province, and passes through the fertile Cibao Valley.

The Cordillera Central provides the principal watershed and drainage divide for the Dominican Republic; the Yuna has its source along the northern slope of the mountain range.

[7] The Yuna descends from its headwaters running south then west where several streams feed into the river near the San José de Ocoa province border.

The Yuna receives its principal tributary, the Camú River, approximately 11.60 km (7.21 miles) northeast of Cotuí at the Duarte Province line at an elevation of 30 m (98.43 feet) above sea level.

The Camú River has its source within the Cordillera Central and has a watershed that spans seven provinces: La Vega, Santiago, Monseñor Nouel, Hermanas Mirabal, Sánchez Ramírez, and Duarte.

The Yuna turns east after receiving the Camú River along its left bank and now serves as the Sánchez Ramírez-Duarte Province line, heading into wetlands filled with rice and cocoa cultivation.

The Yuna continues to decrease in elevation as it heads east reaching 24 m (78.74 feet) above sea level upon entering Duarte Province and the municipality of Eugenio Maria de Hostos where it meets two small tributaries along its left bank: the Nigua and Yaiba Rivers.

The Yuna then traverses a region with several lagoons and wetlands and heads north to the town of Villa Riva before turning southeast and receiving the Payabo River on its right bank.

The main branch of the Yuna continues northeast receiving the Guayabo River on its left bank before traveling east into Samaná Province.