The restoration of migration pathways for fish is crucial for the maintenance of populations in a worldwide context of increasing river fragmentation due to the development of dams. Studies aiming at quantifying fish passage at dams through fishway efficiency estimates concern few species, mostly diadromous. Data are lacking regarding most potamodromous species, despite their need to move to complete their life cycles. This study aimed to evaluate the efficiency of two vertical slot fishways for upstream fish migration on two consecutive run-of-the-river hydropower dams (Verbois and Chancy-Pougny) on the Rhône River. Radiotelemetry and PIT-tagging were used together (1) to describe the behaviour of fish under the dams and (2) to quantify entrance probability and passage efficiency of the fishways, for three potamodromous, partially migratory species, comprising of two cyprinids (Barbus barbus and Squalius cephalus) and one salmonid (Salmo trutta). The study revealed that fish preferentially moved upstream of the dam beside the gates, independently of their opening, rather than in the main flow of the turbines. While the passability of fishways did not differ among species (68% for all species), the attractiveness was dependent on the dam/fishway, the species and some individual characteristics such as fish body length and condition. A few fish remained below the gates or near the fishway for a long time, up to several months, without being able to detect the entrance. Overall, results revealed a lower efficiency of the fishways for trout than for the two cyprinids. Attraction was pointed out as the major limiting factor to the efficiency of the Verbois fishway for barbel and trout. Overall, results suggested to better account for fish motivation (migratory behaviour) to assess fishway efficiency for these species.