The river flows through the municipal territories of Horní Brusnice, Pecka, Borek, Tetín, Miletín, Rohoznice, Červená Třemešná, Hořice, Jeřice, Cerekvice nad Bystřicí, Hněvčeves, Benátky, Sovětice, Sadová, Dohalice, Mžany, Mokrovousy, Třesovice, Nechanice, Kunčice, Boharyně, Puchlovice, Roudnice, Kratonohy, Kosičky, Kosice, Písek, Nové Město and Chlumec nad Cidlinou.

A survey conducted in 2010 showed that the Bystřice River was inhabited by a total of 21 species of aquatic molluscs, out of which 11 were gastropods and the remaining 10 were bivalves.

On the other hand, there was also the discovery of the presence of the endangered thick shelled river mussel, with an increased population density of the species as compared to a few years ago.

[5] The river in the valley to the west of Hořice, along with its immediate surroundings, is protected as the Údolí Bystřice nature monument.

[6] The river valley on its upper course is protected as the Kalské údolí nature monument.