A fully automated method for the detection and quantification of bird migration was developed for operational C-band weather radar, measuring bird density, speed and direction as a function of altitude. These weather radar bird observations have been validated with data from a high-accuracy dedicated bird radar, which was stationed in the measurement volume of weather radar sites in The Netherlands, Belgium and France for a full migration season during autumn 2007 and spring 2008. We show that weather radar can extract near real-time bird density altitude profiles that closely correspond to the density profiles measured by dedicated bird radar. Doppler weather radar can thus be used as a reliable sensor for quantifying bird densities aloft in an operational setting, which—when extended to multiple radars—enables the mapping and continuous monitoring of bird migration flyways. By applying the automated method to a network of weather radars, we observed how mesoscale variability in weather conditions structured the timing and altitude profile of bird migration within single nights. Bird density altitude profiles were observed that consisted of multiple layers, which could be explained from the distinct wind conditions at different take-off sites. Consistently lower bird densities are recorded in The Netherlands compared with sites in France and eastern Belgium, which reveals some of the spatial extent of the dominant Scandinavian flyway over continental Europe.