The Guadix Basin is located on the ancient contact between the two main structural realms of the Betic Cordillera (S. Spain): the Internal Zone (or Alboran Block) and the External Zone (corresponding to the folded and faulted South Iberian paleomargin). During the continental stage of infilling (Late Tortonian-Late Pleistocene) the basin was an endorheic depression, with a large shallow lake, acting as local base level in the eastern sector, and three well developed main alluvial systems (one axial and two transverse) in the western part. The interplay between subsidence and sediment supply from the transverse alluvial fans gave way temporarily to the blocking of the master drainage towards the east resulting in shallow ephemeral lakes occupying the axial valley. Next to the connection with the ephemeral lakes, the floodplain deposits of the Axial valley, formed by detritical and carbonate sediments, host a number of important macromammal fossil sites characterizing the transition between the Pliocene and the Pleistocene and evidencing an important faunistical dispersion. We advance here the results of the characterization of those carbonate sediments, showing that most of them were deposited in palustrine environments. Several facies have been established according to their exposure index, as inferred by the degree of pedological modifications affecting the original sediments, and by its content in detrital components. Some other carbonate bodies, that are exposed also in the studied area, have been interpreted as tufas and as calcretes.