The São Domingos area (Corte do Pinto, Portugal) represents a large sulfide ore deposit in the Iberian Pyrite Belt that was mined primarily for copper and sulfur in the past. Currently, the deserted mine and mine wastes are the reason for the production of acid mining drainage releasing potentially harmful elements. Because metastable secondary sulfates may temporary sink toxic pollutants, the in situ monitoring of their distribution is required. In this work, we tested a handheld Raman spectrometer equipped with a 532 nm laser excitation for this task. Twelve selected samples of complex composition were analyzed directly in the field using the handheld Raman spectrometer. For comparison, the collected samples were additionally analyzed through laboratory‐based Raman spectroscopy and X‐ray diffraction. Based on the in situ measurements, rozenite, melanterite, coquimbite, jarosite, metavoltine, chalcanthite, bonattite, antlerite, halotrichite‐group minerals, gypsum, and sulfur were detected. The results show that handheld Raman spectrometer is comparable with other laboratory techniques and such handheld systems can be deployed successfully for monitoring of sulfate distribution directly on site.