Saharan oases are frequently subjected to waterlogging due to the presence of shallow and salty groundwater and poor irrigation and drainage conditions. To overcome this problem in Tunisia, in 2002 an official modernization programme was implemented based on two operations: (i) increasing irrigation efficiency by building concrete irrigation canals to limit losses due to water percolation and (ii) controlling waterlogging and salinity by installing a subsurface drainage system in place of the traditional open-ditch system. In this study, a salinity balance was performed in Fatnassa, a representative Saharan oasis in Tunisia. Two spatial levels were monitored over a period of two years: an irrigated and drained field (0.8 ha) and the northern part of the oasis covering 114 ha. Results showed an equilibrated salinity balance at the field level, whereas, at the oasis level, the drainage system was unable to evacuate more than 30% of the salts in the first year and 15% in the second. We consider the clogging effect detected in several locations in the oasis as the main cause of this dysfunction. For the future, we recommend a more participatory approach to designing drainage systems, probably moving toward mixed systems with traditional open ditches and modern subsurface pipes, both easy to maintain by the farmers themselves. Adequate envelopes to prevent clogging in mineral soils have to be tested in situ before extension of subsurface drainage.