We analyze optical and X-ray observations of GRB 050904 obtained with TAROT and SWIFT. We perform temporal and spectral analysis of the X-ray and optical data. We find significant absorption in the early phase of the X-ray light curve, with some evidence (3 sigma level) of variability. We interpret this as a progressive photo-ionization. We investigate the environment of the burst and constrain its density profile. We find that the overall behavior of the afterglow is compatible with a fireball expanding in a wind environment during the first 2000 seconds after the burst (observer frame). On the other hand, the late (after 0.5 days, observer frame) afterglow is consistent with an interstellar medium, suggesting the possible presence of a termination shock. We estimate the termination shock position to be R_t ~ 1.8 x 10^{-2} pc, and the wind density parameter to be A_* ~ 1.8. We try to explain the simultaneous flares observed in optical and X-ray bands in light of different models : delayed external shock from a thick shell, inverse Compton emission from reverse shock, inverse Compton emission from late internal shocks or a very long internal shock activity. Among these models, those based on a single emission mechanism, are unable to account for the broad-band observations. Models invoking late internal shocks, with the inclusion of IC emission, or a properly tuned very long internal shock activity, offer possible explanations.