We investigate the effect of decoherence on Fano resonances in wave transmission through resonant scattering structures. We show that the Fano asymmetry parameter q follows, as a function of the strength of decoherence, trajectories in the complex plane that reveal detailed information on the underlying decoherence process. Dissipation and unitary dephasing give rise to manifestly different trajectories. Our predictions are successfully tested against microwave experiments using metal cavities with different absorption coefficients and against previously published data on transport through quantum dots. These results open up new possibilities for studying the effect of decoherence in a wide array of physical systems where Fano resonances are present.