The Río Negro flows along the southern border of the department, forming the natural border with the departments of Durazno to the southeast and Soriano to the south.
Tributary streams (arroyos) to the Río Negro, flow through most of the department.
From east to west, these are: Arroyo Salsipuedes Grande, which forms part of the border with Tacuarembó Department to the east, while its tributary Arroyo Juan Tomas forms a little part of the northeast border with Paysandú Department, Arroyo Tres Árboles with its tributary Arroyo Islas de Argüelles, Arroyo Rolón, Arroyo Grande, with its tributaries Arroyo de las Flores and Arroyo Averías Grande, Arroyo Don Esteban Grande, Arroyo Sanchez Grande, with its tributaries Arroyo Sanchez Chico and Arroyo Coladeras.

The Río Negro discharges into Río Uruguay about 32 kilometres (20 mi) southwest of Fray Bentos.
Notable along its course in respect to this department are two hydroelectric dams: the Rincón de Baygorria Dam, forming the Baygorria Reservoir and the Constitución Dam (also known as Palmar Dam), forming the Paso de Palmar Reservoir.
In both cases, the power installations are situated on the neighbouring departments of Durazno and Soriano respectively.

A big part of the north border with Paysandú Department is formed by Arroyo Negro with two of its tributary streams flowing through the northwest of the department.
These are: Arroyo Gutiérez Grande and Arroyo Bellaco.
It discharges into Río Uruguay about 21 kilometres (13 mi) north of San Javier and opposite the city of Argentina Concepción del Uruguay, forming at its mouth a sandy beach named Playa Arroyo Negro.
There is also Arroyo Romàn Grande, which discharges directly into Río Uruguay.
Several sandy islands are formed in the curve of Río Uruguay upstream of Fray Bentos between Uruguay and Argentina.

On the northeast part of the department starts the big hill range Cuchilla de Haedo, which extends to the northeast forming its highest levels between the departments of Salto and Rivera.
The hill Cerro del Quebracho is part of this range.
The second and smaller hill range, in the west part of the department, is the Cuchilla de Navarro.
Independent of these ranges, the hill Cerro Pelado is in the middle south, and the hills Cerro Colorado and Cerro Malvenir are southeast of Fray Bentos.
The Río Negro flows along the southern border of the department, forming the natural border with the departments of Durazno to the southeast and Soriano to the south. Tributary streams (arroyos) to the Río Negro, flow through most of the department. From east to west, these are: Arroyo Salsipuedes Grande, which forms part of the border with Tacuarembó Department to the east, while its tributary Arroyo Juan Tomas forms a little part of the northeast border with Paysandú Department, Arroyo Tres Árboles with its tributary Arroyo Islas de Argüelles, Arroyo Rolón, Arroyo Grande, with its tributaries Arroyo de las Flores and Arroyo Averías Grande, Arroyo Don Esteban Grande, Arroyo Sanchez Grande, with its tributaries Arroyo Sanchez Chico and Arroyo Coladeras.
The Río Negro discharges into Río Uruguay about 32 kilometres (20 mi) southwest of Fray Bentos. Notable along its course in respect to this department are two hydroelectric dams: the Rincón de Baygorria Dam, forming the Baygorria Reservoir and the Constitución Dam (also known as Palmar Dam), forming the Paso de Palmar Reservoir. In both cases, the power installations are situated on the neighbouring departments of Durazno and Soriano respectively.
A big part of the north border with Paysandú Department is formed by Arroyo Negro with two of its tributary streams flowing through the northwest of the department. These are: Arroyo Gutiérez Grande and Arroyo Bellaco. It discharges into Río Uruguay about 21 kilometres (13 mi) north of San Javier and opposite the city of Argentina Concepción del Uruguay, forming at its mouth a sandy beach named Playa Arroyo Negro. There is also Arroyo Romàn Grande, which discharges directly into Río Uruguay. Several sandy islands are formed in the curve of Río Uruguay upstream of Fray Bentos between Uruguay and Argentina.
On the northeast part of the department starts the big hill range Cuchilla de Haedo, which extends to the northeast forming its highest levels between the departments of Salto and Rivera. The hill Cerro del Quebracho is part of this range. The second and smaller hill range, in the west part of the department, is the Cuchilla de Navarro. Independent of these ranges, the hill Cerro Pelado is in the middle south, and the hills Cerro Colorado and Cerro Malvenir are southeast of Fray Bentos.
Río Negro Department