An important gap in the management of land erosion in mining-affected areas is the understanding of the entire sediment routing system and the links between sources and storage at the catchment scale. In this study, we examine sediment delivery and its seasonality in the nickel mining-affected Santa Cruz and Pamalabawan catchments, in the Philippines. We monitored discharge, suspended sediment concentrations and suspended sediment loads across 13 sub-catchments with contrasting degrees of mining influence from June 2018 to July 2019. First, we show the importance of the size of the area that has been physically disturbed within our sub-catchments, with as little as 10-22% of relative disturbance area being enough to generate fourfold to eightfold increase in the sediment yield relative to less disturbed and pristine areas. We found that sub-catchments with >10% disturbance exhibit the highest sediment yields (15.5 ± 44.7 t km-2 d-1) compared with sub-catchments with <10% disturbance (3.6 ± 17.7 t km-2 d-1) and undisturbed catchments (2.0 ± 5.7 t km-2 d-1). We also show that sediment flushing predominantly occurs in the most disturbed sub-catchments at the onset of the wet season. A small number of flood events transports the bulk of the sediment, with hysteresis effects being most pronounced in disturbed areas. Lastly, we show that floodplain sediment recycling exerts a key control on sediment delivery at both reach and catchment scales, with the relative contribution of floodplain sources to the sediment budget becoming dominant in the latter stages of the wet season, up to 89% of the total sediment export per storm event. This study highlights the importance of both degree of disturbance and sediment pathways in controlling sediment transport in mining-disturbed areas, and that considering the entire sediment routing system, including intermediate stores, is crucial to optimising existing and future measures against siltation and potential contamination of trace metals and metalloids downstream of mining areas.