Emissions and riverine loads of pollutants were estimated for five sub-catchments in the Njoro River Catchment, Kenya to isolate specific areas for interim pollution management. The most vulnerable sub-catchments were the densely settled and heavily farmed areas around Egerton University and Njoro Township with the restricted area between them demonstrating a remarkable potential to retain/remove most of the pollution emitted in the Egerton University area. The least vulnerable sub-catchment was the predominantly forested Upper Njoro River Catchment whereas the recently settled and increasingly farmed Lower Little Shuru was moderately vulnerability. The method provided a scientific framework for the rapid assessment of catchment vulnerability to prioritize areas for remediation.