Acid mine drainage represents an extreme type of water pollution. The environments develop especial hydrochemical and ecological characteristics, such as high concentrations of acidity and low biodiversity, with dominance of acidophilic organisms. Ecological criteria are assuming increasing relevance for assessing water quality, including in acid mine drainage-affected systems. Photosynthetic pigments, like chlorophyll, could be considered in this context as they are generally used to estimate phytoplankton biomass. The present work was focused on acid mine drainage and their relationships with chlorophyll a. It was developed in the historic mine of São Domingos (Iberian Pyrite Belt, SW Europe). The methodological approach comprised two sampling campaigns (October and February) to represent seasonal behaviour. The diversity of hydrological conditions was also considered through sampling sites established in the pit lake, acidic lagoons and affected stream. Hydrochemistry and chlorophyll a were analysed. The obtained results revealed very low pH values, with a minimum of 2.1. In general, hydrochemistry indicates higher concentrations of pollutants in summer. One of the sampling point, located in an acidic lagoon, stood out by highest concentrations, presenting maximum of sulfate (6564 mg/L), As (6.26 mg/L), and metals like Al (675 mg/L), Cd (1,30 mg/L), Zn (199 mg/L). These highest concentrations coincided with the maximum concentration of chlorophyll a (113 μg/L). The results suggested that the more contaminated the environment, more chlorophyll a was produced. Factor analyses emphasised the relationships between acid drainage properties and the photosynthetic activity, indicating a strong pH dependency of chlorophyll a production.Patricia Gomes acknowledges FCT (Science and Technology Foundation, Portugal) by the research fellowship under the POCH (Programa Operacional Capital Humano) supported by the European Social Fund and National Funds of MCTES with reference SFRH/BD/108887/2015. This work was co-funded by the European Union through the European Regional Development Fund, based on COMPETE 2020 - project ICT (UID/GEO/04683/2013) with reference POCI-01-0145-FEDER-007690 and by project Nano-MINENV number 029259. The authors are also deeply grateful to the anonymous reviewers for their valuable comments and suggestions