From 13-years of the spectral optical monitoring of a well-known broad-line radio galaxy 3C 390.3 we concluded that the geometry of the broad emission-line region is complex, while still the main part of the emission is coming from the accretion disk. Here we present part of the analysis of the broad Hα and Hβ emission lines, which are showing highly variable double-peaked profiles during the monitoring period (1995-2007), with the aim to probe the accretion disk properties. The disk-like geometry plays a dominant role, but the variability of Hα and Hβ line profiles and intensities shows a presence of an additional emission-line region, that has a different nature for different periods, e.g. in one period the observed variation can be well modeled if one assumes changes in position and size of the emitting disk along the accretion disk.
