New engineering solutions are required to minimize the impacts raised by the increasing number of anthropogenic barriers on the watercourses. The longitudinal connectivity must be provided through fishways to allow free passage for the whole fish community. Recently, a multi slot fishway (MSF) was developed, with two consecutive vertical slots that divide the overall head drop, thus, reducing the discharge, velocity and turbulence. The present study assessed the effectiveness of a MSF design for two cyprinid species with different ecological traits: the Iberian barbel (Luciobarbus bocagei), a large-bodied potamodromous benthic fish, and the Southern Iberian chub (Squalius pyrenaicus) a small-bodied water-column fish. Experiments were conducted in spring and autumn. Results show differences in the passage performance between seasons and species. During spring, S. I. chub achieved a higher entry efficiency and shorter transit time to fully negotiate the fishway, while for the I. barbel no differences were found. Overall, the MSF offers low operational costs compared to a standard vertical slot fishway (VSF), however, concerns about the entrance and attraction conditions should be addressed. Additionally, due to the lower operational discharge, the propensity for obstruction with woody debris and sediments should not be disregarded.