Intense human activities, particularly industrial and agricultural output, has enriched metal(loid)s in riverine sediment and endangered aquatic ecosystems and human health. Promoting proper river management requires an assessment of the possible ecological hazards and pollution posed by metal(loid)s in sediments. However, there are limited large-scale risk assessments of metal(loid)s contamination in riverine sediment in heavily populated nations like Bangladesh. This study compiled data on sediment metal(loid)s, for example, Cd, As, Cu, Ni, Cr, Pb, Mn, and Zn, from 24 major rivers located across Bangladesh between 2011 and 2022 and applied positive matrix factorization (PMF) to identify the critical metal(loid)s sources and PMF model-based ecological risks. Based on studied metal(loid)s, 12-78% of rivers posed higher contents than the upper continental crust and 8% of the river sediments for Cr and Ni, whereas 4% for Cd and As exceeded probable effect concentration. Cr and Ni in the sum of toxic units (STU), whereas Mn, As and Cd in potential ecological risk (PER) posed the highest contribution to contaminate sediments. In the studied rivers, sediment contaminant Mn derived from natural sources; Zn and Ni originated from mixed sources; Cr and Cu were released from the tannery and industrial emissions and Cd originated from agricultural practices. Source-based PER and NIRI indicated that mixed source (4% rivers) and tannery and industrial emission (4% rivers) posed very high risks in sediments. For the creation of macroscale policies and the restoration of contaminated rivers, our national-scale comprehensive study offers helpful references.