The Subaé river watershed is considered one of the most critical Pb-impacted environments in Brazil and around the world, due to pollutant dispersion during 33 years of lead ore purification in Santo Amaro da Purification. Severe damages have been reported in biota and population, which depends on the Subaé river watershed quality for agriculture, fishing, and shellfish harvesting. This study aims to understand the geochemical characteristics and dynamics of the river close to the former Pb smelter. The river was sampled at eight sites upstream and eight sites downstream the smelter, near the estuary in the Todos os Santos Bay, six times during a year. Immediate analyses were performed by multiprobe. Major ions were measured by chromatography, dissolved metals by ICP-OES in the filtrated samples (0.45 μm), and particulate metals > 0.45 μm by EDX spectrometry. The ions Na⁺ and HCO3⁻ are dominated in the river. Most of the samples (47.6%) were classified as sodic, due to oceanic saline intrusion during tide. Despite the high pollution caused by the smelter from 1960 to 1993, still observed in the surrounding soils, dissolved and particulate metals in the river remained low in all sites during the entire year. Only Cu presented some concentration above the threshold of the Brazilian regulations. The discharge of metals by the river into the Todos os Santos Bay appears to be low for Pb and Zn (2.2 and 14.3 kg km⁻¹ year⁻¹, respectively), but higher for Cu comparatively to other worldwide bays.