Size-frequency data were collected for two rheophilic fish species, Cottus perifretum and Leuciscus cephalus, at the confluences of 18 lowland tributaries along the regulated River Meuse (the Netherlands) between May 2004 and April 2005. Cottus perifretum is a resident species, using these stream mouth habitats throughout its entire life: i.e. as a spawning, nursery and adult habitat. Leuciscus cephalus is a transient species that uses these stream mouth habitats only as a temporary 0+ juvenile habitat during fall and early winter. This study suggests that the stream mouth habitats along the River Meuse fulfil different ecological functions for C. perifretum and L. cephalus.