Manganese occurs naturally in sediment, yet anthropogenic sources, such as industrial wastewater and mining, increases Mn concentration. However, the environmental risk of bioavailable Mn is often overlooked and infrequently addressed. A probabilistic risk assessment was conducted to determine the effects of bioavailable Mn in river sediments on reproduction in model organism Caenorhabditis elegans using in utero egg counts and germline apoptosis as biomarkers. The lowest-observed-adverse-effect level (LOAEL) of sediment Mn that decreases in utero egg counts or increases germline apoptosis in C. elegans was 50 or 10 mg of Mn(II) per kg of dry weight sediment, respectively. Effect and exposure analyses were conducted using Hill model-simulated concentration-response curves and Mn concentrations of Laojie River sediment. Risk quotients (RQs) and exceedance risk (ER) analyses showed that bioavailable levels of Mn in Laojie River sediments from downstream sites collected during the dry season elevate reproductive risk as measured by germline apoptosis. These findings suggest that bioavailable levels of Mn in sediment exert negative impacts, and germline apoptosis is a sensitive biomarker for reproductive risk assessment. Our results also suggest that the anthropogenic Mn pollution in river sediment and spatial-seasonal bioavailability of Mn should be considered to improve sediment quality control.