The North Rupununi District in south-west Guyana is comprised of a mosaic of ecosystems, including savannas, wetlands and forests, and is home to the Makushi Amerindians, who depend on the waterways for their subsistence needs. With logging and mining seen as increasing threats to the region, it is necessary to look at methods for engaging stakeholders in monitoring the status of their natural resources. This paper presents the results of a pilot study carried out to investigate water use by the Makushi Amerindians, and collect baseline data on the hydro-morphological aspects of the waterways. Methods included informal interviews, the use of the River Habitat Survey (RHS), and water quality measurements. The results indicate the heavy reliance of the Makushi on the waterways for their daily lives, particularly on fishing. Although ponds and creeks are important sources of fish, the rivers provide much larger catches of a greater diversity of fish species, both in the wet and dry seasons. The physical characteristics of the water sources used by the Makushi are mainly associated with the surrounding habitat types: the savanna areas containing the more nutrient rich whitewater rivers, and the tropical forest areas containing the less nutrient rich black-water rivers. This study indicates that at present there is no direct evidence of adverse impacts on the waterways used by the Makushi in terms of fish catches, habitat conditions and water quality. A monitoring scheme was set up using this study's outputs as a baseline from which any future changes can be compared. Further work is to be carried out over the next three years to produce monitoring and sustainable management procedures for the North Rupununi ecosystems, by linking the physical attributes of the environment to biodiversity and subsequently local livelihoods, and by building capacity of local stakeholders through training.