This paper presents the effects of flooding on the accumulation of manganese (Mn) in soils within proximity of the Boac and Mogpog rivers in Marinduque of The Philippines. Marinduque, an island province in the Philippines, experienced two catastrophic tailings storage facility (TSF) failures in the 1990s that released sulfide-rich tailings into the two major rivers. The Philippines experiences 21–23 typhoons every year, 11 of which pass thru Marinduque that causing inundation of floodplain areas in the province. A flood hazard map developed using LiDAR DEM was utilized for the Boac and Mogpog rivers for an accurate representation of flooding events. A portable X-ray fluorescence spectrometer (pXRF) and a Hannah multi-parameter device were used for the on-site analyses of Mn concentration and water physico-chemical properties, respectively. Spatial grid mapping with zonal statistics was employed for a comprehensive analysis of all the data collected and processed. Correlation analysis was carried out on Mn concentrations in soil and surface water, electrical conductivity (EC), total dissolved solids (TDS), pH, temperature, curve number (CN), and flood heights. The curve number indicates the runoff response characteristic of the Mogpog-Boac River basin. The results show that 40% of the total floodplain area of Boac and Mogpog were subjected to high hazards with flood heights above 1.5 m. The Mn content of soils had a statistically significant moderate positive correlation with flood height (r = 0.458) and a moderate negative correlation with pH (r = −0.438). This condition suggested that more extensive flooding promotes Mn contamination of floodplain soils in the two rivers, the source of which includes the mobilization of Mn-bearing silt, sediments, and mine drainage from the abandoned mine pits and TSFs. There is also a strong negative correlation between pH and Mn concentrations in surface water, a relationship attributed to the solubilization of Mn-bearing precipitates based on geochemical modeling results. Using Muller’s geo-accumulation index, 77.5% of the total floodplain of the two rivers was identified as “moderately contaminated” with an average Mn soil content of 3.4% by weight (34,000 mg/kg). The Mn contamination map of floodplain soils in the Mogpog and Boac rivers described in this study could guide relevant regional, national, and local government agencies in planning appropriate intervention, mitigation, remediation, and rehabilitation strategies to limit human exposure to highly contaminated areas.