Negative affects? No, as the stuff you see growing on rocks in river may be moss or it may be harmless algae. All part of a completely natural ecosystem. There honestly is nothing harmful to fish from either although many aquarium owners may find 'true' algae types such as hair algae unsightly and it can be detrimental to aquatic plants.
Cyanobacteria are not a 'true' algae in the sense the OP is inquiring about but rather a photosynthetic bacteria that are capable of acquiring energy from light. Not all of cyano is bad either but some strains are capable of producing toxins that can have damaging or even lethal effects to many creatures that encounter it.