While great strides have been made in collecting presence data and developing accurate species distribution models, much less is known about the migratory process that guides the spatio-temporal changes in distributions for migrating species, especially birds. In this work, we address a challenging inference task, where given only aggregate and noisy data of the volume of birds for each spatial pixel and time window, we predict the likely transition links with their associated probabilities. We propose a framework to build such migration networks for different bird species and present a real world example of constructing a network using our approach.