Heavy metals (HMs) in suspended particulate matter (SPM) present critical ecological and health concerns due to their mobility, bioavailability, and toxicity in aquatic systems. However, the speciation and associated ecological risks of HMs in freshwater SPM remain inadequately characterized. This study investigated the concentrations, speciation, and ecological risks of ten HMs (Cr, Ni, Cu, Zn, As, Cd, Pb, Mn, V, and Co) in paired SPM-sediment matrices across five representative small and medium-sized lacustrine and fluvial ecosystems in Southwest China, using a modified European Community Bureau of Reference (BCR) sequential extraction method combined with multiple risk assessment approaches. Results showed that Mn exhibited the highest enrichment in SPM, with concentrations 8.8-fold higher in lake systems and 2.6-fold higher in river systems compared to sediments. BCR analysis further revealed that, compared to sediments, SPM had a higher proportion of reducible fractions, implying the presence of substantial amounts of recently formed, authigenic Mn oxides in SPM. Geoaccumulation index (Igeo) indicated that Cd, Mn, and Zn were the predominant contaminants in SPM across all systems. These three metals exhibited the highest proportions in the exchangeable fraction, and SPM contained greater exchangeable fractions than sediments, suggesting enhanced mobility and bioavailability. Multidimensional risk assessment demonstrated that SPM-associated metals, especially Mn, posed greater ecological and health risks (particularly for children) than those in sediments. Overall, this study highlights SPM as both a carrier and a secondary source of HMs in freshwater systems, underscoring the need for targeted monitoring and management strategies to reduce labile HM inputs and protect aquatic ecosystem health.