The wellbeing, socio-economic viability and the associated health of the inhabitant species of any ecosystem are largely dependent on the quality of its water resources. In this regard, we developed a protocol to measure the potential impact of various environmental and anthropogenic factors on runoff quality at 22 water sampling sites across the Bumbu Watershed in Papua New Guinea. For this purpose, we utilized Digital Elevation Models and several GIS techniques for delineation of stream drainage patterns, classification of the watershed based on Land Use/Land Cover, spatial interpolation of rainfall patterns and computation of the corresponding factor runoff. Our study concludes that a variety of potential challenges to surface water quality are possible such as natural geologic and geochemical inputs, runoff accumulation of precipitation and organic matter pollutants. The developed protocol can also accommodate socio-economic factors such as community and household health, sanitation and hygiene practices, pollution and waste disposal. This research lays the foundation for further development of an all-inclusive correlational analysis between the relative importance values of the factors influencing runoff and spatially distributed water quality measurements in the Bumbu basin.