Complete hydrological time series are necessary for water resources management and modeling. This can be challenging in data scarce environments where data gaps are ubiquitous. In many applications, repetitive gaps can have unfortunate consequences including ineffective model calibration, unreliable timing of peak flows, and biased statistics. Here, Direct Sampling (DS) is used as a non-parametric stochastic method for infilling gaps in daily streamflow records. A thorough gap-filling framework including the selection of predictor stations and the optimization of the DS parameters is developed and applied to data collected in the Volta River basin, West Africa. Various synthetic missing data scenarios are developed to assess the performance of the method, followed by a real-case application to the existing gaps in the flow records. The contribution of this study includes the assessment of the method for different climatic zones and hydrological regimes and for different upstream-downstream relations among the gauging stations used for gap filling. Tested in various missing data conditions, the method allows a precise and reliable simulation of the missing data by using the data patterns available in other stations as predictor variables. The developed gap-filling framework is transferable to other hydrological applications, and it is promising for environmental modeling.