This review focuses on the challenges that need to be addressed to increase knowledge on the distribution, transport and biogeochemical reactions of contaminants in carbonate media. In order to do so, it has been necessary to review recent studies on contaminants that due to their emerging in- terest and unawareness of their threat to human have not yet been deeply analyzed in carbonate aquifers (e.g.: Dense Non- aqueous Phase Liquids (DNAPLs), light non-aqueous phase liquids (LNAPLs), Volatile Organic Compounds (VOCs), Path- ogens, Contaminants of Emerging Concern (CECs), Micro- and Nanoplastics and Nanoparticles). To this end, it seems necessary to progress along two lines: (1) a methodological line, in which the advance must be achieved in the field of distribution of heterogeneous elements in carbonate forma- tions and in early detection and warning systems; and (2) a more scientific line, in which specific studies of emerging pol- lutants might produce an advance in the development of flow and transport models in heterogeneous and anisotropic media.