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During the 1970s and 1980s, West Africa has faced extreme climate variations with extended drought conditions. Of particular importance is the Niger basin, since it traverses a large part of the Sahel and is thus a critical source of water for an ever-increasing local population in this semi arid region. However, the understanding of the hydrological processes over this basin is currently limited by the lack of spatially distributed surface water and discharge measurements. The purpose of this study is to evaluate the ability of the ISBA-TRIP continental hydrologic system to represent key processes related to the hydrological cycle of the Niger basin. ISBA-TRIP is currently used within a coupled global climate model, so that the scheme must represent the first order processes which are critical for representing the water cycle while retaining a limited number of parameters and a simple representation of the physics. To this end, the scheme uses first-order approximations to account explicitly for the surface river routing, the floodplain dynamics, and the water storage using a deep aquifer reservoir. In the current study, simulations are done at a 0.5 by 0.5A degrees spatial resolution over the 2002-2007 period (in order to take advantage of the recent satellite record and data from the African Monsoon Multidisciplinary Analyses project, AMMA). Four configurations of the model are compared to evaluate the separate impacts of the flooding scheme and the aquifer on the water cycle. Moreover, the model is forced by two different rainfall datasets to consider the sensitivity of the model to rainfall input uncertainties. The model is evaluated using in situ discharge measurements as well as satellite derived flood extent, total continental water storage changes and river height changes. The basic analysis of in situ discharges confirms the impact of the inner delta area, known as a significant flooded area, on the discharge, characterized by a strong reduction of the streamflow after the delta compared to the streamflow before the delta. In the simulations, the flooding scheme leads to a non-negligible increase of evaporation over large flooded areas, which decreases the Niger river flow by 15% to 50% in the locations situated after the inner delta as a function of the input rainfall dataset used as forcing. This improves the simulation of the river discharge downstream of the delta, confirming the need for coupling the land surface scheme with the flood model. The deep aquifer reservoir improves Niger low flows and the recession law during the dry season. The comparison with 3 satellite products from the Gravity Recovery and Climated Experiment (GRACE) shows a non negligible contribution of the deeper soil layers to the total storage (34% for groundwater and aquifer). The simulations also show a non negligible sensitivity of the simulations to rain uncertainties especially concerning the discharge. Finally, sensitivity tests show that a good parameterization of routing is required to optimize simulation errors. Indeed, the modification of certain key parameters which can be observed from space (notably river height and flooded zones height changes and extent) has an impact on the model dynamics, thus it is suggested that improving the model input parameters using future developments in remote sensing technologies such as the joint CNES-NASA satellite project SWOT (Surface Water Ocean Topography), which will provide water heights and extentat land surface with an unprecedented 50-100 m resolution and precision.