Plastic litter is increasingly accumulating in the marine environment, with rivers considered key pathways for entry. Current estimations of plastic input into the sea from land-based sources are limited in accounting for the mobilization and transport of plastic generated in the whole catchment area or in considering local variations in waste handling practices. Here, we show that, with an integrated discharge modeling approach (based on actual rainfall and local estimates for exposed mismanaged plastic waste), more realistic temporal estimates of plastic discharges into the sea can be constructed. Applying this approach to Indonesia enabled us to estimate the total national inputs of plastic waste into the sea from rivers and coasts and how these vary with rainfall, while providing insight into those catchments, local communities, and waste handling practices that most contribute to plastic waste leakages. We found that the plastic fluxes vary significantly in both the short and long term and that the total amount of plastic waste discharged during wet years may be twice as much as during dry years. Furthermore, river size, catchment population density, local waste management, and proximity of point sources influence river plastic waste loads. Such an integrated assessment can be very effective in helping to prioritize where interventions are most needed and, in combination with frequent monitoring, can provide evidence of the impact that upstream measures have on preventing plastic inputs into the sea.