Long-term exposure to atmospheric fine particulate matter (PM2.5) is a major human health concern; respiratory and cardiovascular diseases are the main consequences. In this study, we present the source apportionment of PM2.5 in a large port region in the South Atlantic, located in a Natural Heritage Estuary, which is a particularly sensitive ecosystem and a marine protected area. The PM2.5 mean concentration was 15.26 ± 7.5 µg m− 3, with a range from 0.7 to 41.0 µg m− 3, exceeding both World Health Organization target thresholds 3 and 4, as well as the Air Quality Guideline level. Notably, 10% (n = 34) of the samples exceeded the Brazilian environmental quality threshold for PM2.5 24-hour mean (25 µg m− 3), which is significant since the guidelines recommend a maximum of 3 to 4 exceedance days per year. Bivariate plots with meteorological data and positive matrix factorization (PMF) were employed to estimate the sources of PM2.5 from soluble ions and trace and major metal compositions. The findings suggest that truck activity in a nearby parking lot is the primary source of PM2.5, and the presence of a transportation structure linked to grain transportation was identified as a secondary source. Additionally, the findings of this study demonstrate an urgent need to address the impact of the Brazilian soybean export industry on human health and biodiversity in the region, given the context of excessive PM2.5 concentrations and the risks they presumably pose.