Markarian 6 is a nearby ( D \sim 78 Mpc ) Seyfert 1.5 , early-type galaxy , with a double set of radio bubbles . The outer set spans \sim 7.5 kpc and is expanding into the halo regions of the host galaxy . We present an analysis of our new Chandra observation , together with archival XMM-Newton data , to look for evidence of emission from shocked gas around the external radio bubbles , both from spatially resolved regions in Chandra and from spectral analysis of the XMM data . We also look for evidence of a variable absorbing column along our line of sight to Mrk 6 , to explain the evident differences seen in the AGN spectra from the various , non-contemporaneous , observations . We find that the variable absorption hypothesis explains the differences between the Chandra and XMM spectra , with the Chandra spectrum being heavily absorbed . The intrinsic N _ { H } varies from \sim 8 \times 10 ^ { 21 } atoms cm ^ { -2 } to \sim 3 \times 10 ^ { 23 } atoms cm ^ { -2 } on short timescales ( 2-6 years ) . The past evolution of the source suggests this is probably caused by a clump of gas close to the central AGN , passing in front of us at the moment of the observation . Shells of thermal X-ray emission are detected around the radio bubbles , with a temperature of \sim 0.9 keV . We estimate a temperature of \sim 0.2 keV for the external medium using luminosity constraints from our Chandra image . We analyse these results using the Rankine-Hugoniot shock jump conditions , and obtain a Mach number of \sim 3.9 , compatible with a scenario in which the gas in the shells is inducing a strong shock in the surrounding ISM . This could be the third clear detection of strong shocks produced by a radio-powerful Seyfert galaxy . These results are compatible with previous findings on Centaurus A and NGC 3801 , supporting a picture in which these AGN-driven outflows play an important role in the environment and evolution of the host galaxy .