Wetlands are widely recognised as the most critical stop-over locations along migration flyways. Wetland ecology is mostly influenced by water levels and water regimes. This research focuses on Bolle di Magadino (Switzerland), an important stop-over site on Lake Maggiore, artificially regulated by a dam. In this work we examined how the artificial flooding of a wetland affects the use of this stop-over site by migrating passerines during spring. Bird presence in the area was evaluated using both data collected at the ringing station located in the wetlands and the bird traffic rate (BTR) supplied by the BirdScan MR1, an avian verticallooking radar (VLR) capable of automatically detecting and classifying birds in flight. In an attempt to shed light on the effect of lake level on stop-over quality, we i) simulated with GIS the extent of the flooded area and of the different habitat categories as the lake level changes; ii) calculated the relationship between lake level and the ability of stop-overing birds to acquire trophic resources; iii) verified that the flux of passerines below 500 m above ground level measured by radar could be used as a proxy for the number of stop-overing birds; iv) calculated the relationship between the number of birds leaving the stop-over and the lake level. While the number of ringed passerines has proven to be representative of the migratory flow below 500 meters of altitude at the site of interest, a high lake level seems to have a negative impact on the use by some species of the Bolle di Magadino area as a stop-over site during spring. In particular, two of the target species -the blackcap and the reed bunting- have proven to be sensitive to higher water levels. While taking into account the limitations and the relative nature of the results, could be necessary for the competent authorities to take these results into consideration in order to safeguard the Bolle di Magadino’s role as an important stop-over area during spring.