Understanding the trade-off between energy expenditure of carrying large fuel loads and the risk of fuel depletion is imperative to understand the evolution of flight strategies during long-distance animal migration. Global flyways regularly involve sea crossings that may impose flight prolongations on migrating land-birds and thereby reduce their energy reserves and survival prospects. We studied route choice, flight behavior, and fuel store dynamics of nocturnally migrating European nightjars (Caprimulgus europaeus) crossing water barriers. We show that barrier size and groundspeed of the birds influence the prospects of extended daylight flights, but also that waters possible to cross within a night regularly result in diurnal flight events. The nightjars systematically responded to daylight flights by descending to about a wingspan's altitude above the sea surface while switching to an energy-efficient flap-glide flight style. By operating within the surface-air boundary layer, the nightjars could fly in ground effect, exploit local updraft and pressure variations, and thereby substantially reduce flight costs as indicated by their increased proportion of cheap glides. We propose that surface-skimming flights, as illustrated in the nightjar, provide an energy-efficient transport mode and that this novel finding asks for a reconsideration of our understanding of flight strategies when land-birds migrate across seas.