The municipality of Amer sits within the catchment basin of the Ter river, which runs along the district’s southern boundary. A tributary of the Ter, the Brugent river runs through the town centre, and is in turn fed by several streams, including those of Can Catau, Castell and Pinyana.

The town of Amer benefits from a network of canals that run through open ditches and, in some sections, through concrete caissons or pipes forming aqueducts.

One of the main waterways here is the Bellvespre canal, located on the west bank of the Brugent, which takes water from a lock situated behind the Hostal Sant Marçal guesthouse. The canal runs parallel to the river until about 130 metres before the Rieral bridge, at which point it turns toward the town centre, where it divides into secondary canals. These works date back to the times of the Benedictine monks at Santa Maria d’Amer monastery. The water was used to run the flour mill—famed throughout the surrounding villages as it produced very fine flour—as well as irrigation systems and the Molí de Bellvespre (Bellvespre Mill) power station. The name Bellvespre came from the family that took over operations after the monks, but the facility was commonly known as the central del Molí (the Mill power station), being the first electric power station in the town and the initial source of power for public lighting here, until the electricity network was sold to the Hidroeléctrica de Cataluña company between 1965 and 1970. A community of local users still depends upon the water from the Bellvespre canal to irrigate their vegetable plots.