Paso Bonito Reservoir (mean depth = 6.5 m; volume = 8.0 × 10^6 m3) is a small raw water reservoir in south-central Cuba. This study evaluated sources of high levels of manganese in the reservoir causing taste and odor problems. Watershed monitoring showed that levels of total manganese (Mn) and total iron (Fe) were high (Mn 0.14–0.64 mg/L; Fe 5.3–12.4 mg/L) during the first flood of the wet season in river sampling stations near historical pyrite mining operations. Monitoring in the reservoir showed that Mn and Fe were present in bottom waters throughout the year, with peak levels (>8 mg/L of Mn and >30 mg/L of Fe) coinciding with low levels of oxygen in summer months. Empirical modeling of Mn concentration in the reservoir water column showed that it correlated significantly with Fe (positive correlation), redox potential (negative correlation) and dissolved oxygen (negative correlation). Statistical evaluation of the temporal cycle of Mn in raw water delivered to the Juan Gonzales Water Treatment Plant showed that Mn accumulation was highly seasonal, peaking annually around September when dissolved oxygen in raw water was at a minimum. Data suggest that during first-flood conditions early in the wet season, mass loading of Mn and Fe from the watershed to the reservoir is high. During the subsequent drier low-flow summer period, external mass loading of metals drops dramatically and the reservoir becomes a large exporter of Mn and Fe as the metals are internally recycled under anaerobic conditions in bottom waters.