In Kenyan rural areas belonging to the Arid and Semi-Arid Lands (ASALs), water quantity and water quality are major issues for the local population. In North Horr Sub-County water quality is threatened by nitrate contamination due to fecal matter pollution. This research, hence, aims at assessing the vulnerability of open shallow water sources to nitrate contamination due to fecal intrusion following flooding events and nitrate percolation in groundwater. The present research, indeed, provides, on one hand, new insights into the analysis of the vulnerability in a scant data context; on the other hand, it assesses the adaptation measures contained in the local development plan. Applying the reference definition of the Intergovernmental Panel on Climate Change (IPCC), the results demonstrate that the open shallow water sources in the northern part of the sub-county are more vulnerable to nitrate contamination. Furthermore, the consistency of the results proves the suitability of the methodology selected. Understanding the vulnerability at the local scale is key to planning risk-reduction strategies as well to increasing the local population’s knowledge about flood-related risks and water quality.