Abstract Land surface processes play an important role in the West African monsoon variability. In addition, the evolution of hydrological systems in this region, and particularly the increase of surface water and runoff coefficients observed since the 1950s, has had a strong impact on water resources and on the occurrence of floods events. This study addresses results from phase 2 of the African Monsoon Multidisciplinary Analysis (AMMA) Land Surface Model Intercomparison Project (ALMIP2), carried out to evaluate the capability of different state-of-the-art land surface models to reproduce surface processes at the mesoscale. Evaluation of runoff and water fluxes over the Mali site is carried out through comparison with runoff estimations over endorheic watersheds as well as evapotranspiration (ET) measurements. Three remote-sensing-based ET products [ALEXI, MODIS, and Global Land Evaporation Amsterdam Model (GLEAM)] are also analyzed. It is found that, over deep sandy soils, surface runoff is generally overestimated, but the ALMIP2 multimodel mean reproduces in situ measurements of ET and water stress events rather well. However, ALMIP2 models are generally unable to distinguish among the two contrasted hydrological systems typical of the study area. Employing as input a soil map that explicitly represents shallow soils improves the representation of water fluxes for the models that can account for their representation. Shallow soils are shown to be also quite challenging for remote-sensing-based ET products, even if their effect on evaporative loss was captured by the diagnostic thermal-based ALEXI. A better representation of these soils, in soil databases, model parameterizations, and remote sensing algorithms, is fundamental to improve the estimation of water fluxes in this part of the Sahel.