West Nile virus (WNV), a mosquito-borne bird virus, drives changes in bird communities and spills over to cause disease in humans and horses. Here we use WNV as a model system for synthesizing heterogeneous data sources to understand ecological systems. Using data from lab experiments, field studies, and citizen science, we tackle three questions: (1) what factors were responsible for the displacement of the original invading strain of WNV in North America by a new virus strain? (2) how do different bird species contribute to the overall transmissibility of WNV within the bird community? (3) More generally, what are the prospects for ecological forecasting of complex systems, and how can we cope with uncertainty in a principled way?