We aim at constraining the geometry of the reprocessing matter in the nearby prototypical Seyfert 2 Galaxy Markarian 3 by studying the time evolution of spectral components associated to the primary AGN emission and to its Compton-scattering. We have analyzed archival spectroscopic observations of Markarian 3 taken over the last 12 years with the XMM-Newton, Suzaku and Swift observatories, as well as data taken during a monitoring campaign activated by us in 2012. The timescale of the Compton-reflection component variability (originally discovered by ASCA in the mid-90s) is ~64 days. This upper limit improves by more than a factor of 15 previous estimates of the Compton-reflection variability timescale for this source. When the light curve of the Compton-reflection continuum in the 4-5 keV band is correlated with the 15-150 keV Swift/BAT curve a delay ~1200 days is found. The cross-correlation results are dependent on the model used to fit the spectra, although the detection of the Compton-reflection component variability is independent of the range of models employed to fit the data. Reanalysis of an archival Chandra image of Markarian 3 indicates that the Compton-reflection and the Fe K-alpha emitting regions are extended to the North up to ~300 pc. The combination of these findings suggests that the optically-thick reprocessor in Markarian 3 is clumpy. There is mounting experimental evidence for the structure of the optically-thick gas and dust in the nuclear environment of nearby heavily obscured AGN to be extended and complex. We discuss possible modifications to the standard unification scenarios encompassing this complexity. Markarian 3, exhibiting X-ray absorption and reprocessing on widely different spatial scales, is an ideal laboratory to test these models (abridged).
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