Nyabarongo River system is an ecosystem that provides goods and services to the Rwandese communities; this river serves as a tributary of the Nile River, an international resource. However, its integrity has been compromised due to increasing pressure for expansion of agricultural land. Against the aforementioned background, the present study was undertaken to assess farmers’ maximum Willingness To Pay (WTP) for protection of Nyabarongo River system. Further, the study assessed the potential influence of different factors on the WTP estimates. A sample of 359 households from four Districts in the catchment area was randomly selected and interviewed through household survey questionnaires. The Contingent Valuation Method (CVM) was applied to estimate the amount of money farmers are willing to pay while the influence of different factors was assessed using the Ordinary Least Squares regression method. Results showed that the mean household’s maximum WTP for the protection of Nyabarongo River system was 486.4 Rwandan francs (Rwf) per household per month over the proposed five years (USD$1 = 607 Rwf). The main factors that were found to have significant statistical influence on the WTP are household income, education of the household head, respondent’s perception of the current quality of water in Nyabarongo River, access to tap water, household size, extension contacts, initial bid amount and knowledge of individual responsibility in wetland protection. Based on these findings, it may be concluded that riparian communities attach considerable economic value to the river system. In order to achieve sustainable management of the wetland, there is need to increase awareness through radios, trainings, extension services and there is a possibility of raising funds from these communities for continued wetland protection