Twenty-three water dams located in the Iberian Pyrite Belt were studied during March 2012 (early spring) in order to carry out an environmental assessment based on diatom communities and to define the relationships between these biological communities and the physico-chemical characteristics of the dam surface water. This is the first time that a diatom inventory has been done for dams affected by acid mine drainage (AMD) in the Spanish part of the Iberian Pyrite Belt (IPB). It was found that the pH was the main factor influencing the behaviour of the diatom communities. Then, using a dbRDA approach it was possible to organize the aggrupation of diatoms into four groups in response to the physico-chemical conditions of the ecosystem, especially pH: (1) Maris, Aac, Gos, Cmora (pH 2–3); (2) Andc, San, And, Dpin (pH 3–4.5); (3) Gran, Pleon, Oliv, Lagu, Chan, SilI, SilII, Joya, Gar, Agrio, Camp, Corum (pH 4.5–6); (4) Herr, Diq I, Diq II (pH 6–7). The obtained results confirmed the response of benthic diatom communities to changes in the physico-chemical characteristics of surface water, and helped to understand the role of diatoms as indicators of the degree of AMD contamination in those 23 dams. Special attention was given to those that have an acidophilic or acid-tolerant profile (pH 2–3 and pH 3–4.5) such as Pinnularia aljustrelica, Pinnularia acidophila, Pinnularia acoricola and Eunotia exigua, which are the two groups found in the most AMD contaminated dams.