The sea lamprey (Petromyzon marinus L.) can be considered an engineer species, as it can substantially modify the river beds where it spawns. Sea lampreys dig nests by removing large volumes of cobbles to create a pit, and leaving them in a mound downstream, thus altering local bed morphology. Previous studies showed that sea lamprey nest-building behaviour increases riverbed heterogeneity in depth and water velocity, which in turn promotes macroinvertebrate diversity. Based on that finding, our study aimed at assessing whether these changes promoted ecosystem functioning. We measured multiple ecosystem functions (biofilm accretion, phosphate and ammonium uptake, and litter breakdown) on the pit and the mound of 30 lamprey nests, as well as on 30 unmodified sites. In spite of the physical and biological heterogeneity, all processes measured showed no differences among sites, pointing towards a complex relationship between physical heterogeneity, biodiversity and ecosystem function.