While the decrease in flow is obvious in the Kikuletwa River, the mechanism leading to the decrease is unclear. We assessed the influence of vegetation cover change on dry season flow in the Kikuletwa River. The combined cover of closed and open forests decreased by 68% while closed and open forests decreased by 56% and 64% respectively. Land under agroforestry decreased by 25%, while that under annual crops increased by 41%. Grasslands increased by 116% and riverine vegetation decreased by 53%. Daily dry season flow showed a slightly decreasing trend in one of the stations despite all of them receiving water from the Rundugai natural springs. On the other hand, low flow indices indicated no statistically significant changes in the long-term average flow and there was no identifiable change in the rainfall amount. The majority (93%) of the local people perceived a changing rainfall pattern and decline in dry season flow in the Kikuletwa River. Changes in the dry season flow then can be associated with the identified land cover changes. Further research to substantiate the local people perceptions is important as indigenous knowledge may be good evidence for ascertaining changes in the natural environment.