The study of acid rock and mine (ARD and AMD) environments mainly focused on the mineralogical and microbiological conditions and responses of such systems. Most of the research that involved some organic viewpoint was related to the amelioration of the environmental conditions, sometimes with contradictory results. How organic matter (OM) participates and which organic fractions are involved in ARD and AMD processes remain unclear.In this work we have applied organic geochemistry tools combined with mineralogical ad molecular microbiology techniques to study of ARD and AMD environments. The main objectives were to identify and characterise the natural sources of OM occurring both at ARD and AMD sites, and to determine whether the OM sources identified are involved in the generation or amelioration of AMD/ARD. This study shows that multiple OM sources occur naturally in acid drainage environments, included plant derived material and mature, petroleum-derived hydrocarbons, originating from the source rocks, apparently have not directly influence on the processes. This suggests that the generation of ARD and AMD is a completely chemoautotrophic process.Particle size of the iron phases present at ARD sites seems to be involved in the iron bioavailability. The presence of goethite in ARD/AMD systems may have a relationship with the presence of OM. Stimulation of ARD sediments using plant derived OM, abundantly present in and around ARD and AMD ponds systems does not result in the neutralisation of ARD or AMD. This suggests that plant material is not used by Fe(III)-reducing bacteria. However, it fuels fermentation processes and it is likely that fermentation products such as acetate, detected in microcosms and in situ, could limit Fe(III)-reduction. In contrast, the stimulation of ARD sediments using manure (particularly sheep manure) raises the pH up to near neutral conditions. Although it remains unclear which OM fraction from the manure is actively involved in the neutralisation of ARD; these results suggest that manure may make an interesting and non-expensive electron donor in AMD/ARD treatments.