AbstractPassive treatment systems are a sustainable solution to mine drainage remediation, however, clarity lacks in the detailed understanding of the geochemical processes that govern the remediation processes. A study was carried out at Shojin River in Southwest Hokkaido, Japan, which has an acidic pH and is high in Fe, to represent the principal processes that occur in mine drainages of similar characteristics. At Shojin, Fe and S were mined from the Shojingawa mine, after which, wastewater contaminated by toxic elements such as Fe, As and Pb continue to flow from the underground. This wastewater flows through industrial and fishing areas, hence ensuring that the water meets environmental standards is important. In particular, the role of colloidal materials in transporting the toxic elements was investigated by analyzing the distribution of the elements (Fe, As and Pb) in the drainage as the dissolved and colloidal fractions, obtained from micro‐, and ultrafiltration respectively. Iron, particularly schwertmannite colloid formation was observed in the Shojin River system. Itwas present in the dissolved fraction in the wastewater like As, but after mixing with the uncontaminated river water, Fe in the colloid fraction gradually increased toward the downstream. Arsenic trends are similar to those of iron, indicating efficient sequestration by the schwertmannite colloids. Lead is dominantly in the dissolved fraction throughout the drainage and is comparatively less sequestered due to competitive adsorption with As and its pH dependence to be efficiently adsorbed. A detailed observation of the concentration trends suggests that pH 3.1 may efficiently allow colloid formation and subsequently, toxic element sequestration. The behavior of Fe colloids in Shojin River was compared to those of a circum‐neutral drainage system (Ainai mine drainage). The formation of the colloids in the acidic system was limited by the pH range, while colloids formed faster and more abundantly in the circumneutral system. The acidic and circum‐neutral systems are abundant in schwertmannite and ferrihydrite colloids respectively. The colloids in both systems were transported after their formation, however, the colloids in the Shojin (acidic) system were transported further than those of the circumneutral system. Aggregation is observed in both systems which results in a deposition of the colloid aggregates and hence an efficient removal of Fe and As, and minimally, Pb from the mine drainages.