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A study that tests the applicability and consistency of independent but complementary approaches in the assessment of interactions between surface water and shallow groundwater within a water-stressed basin is described. The mostly agricultural Limari basin in arid north-central Chile was chosen as a suitable case study. The analyses involved: (1) a connectivity index method, (2) hydrochemistry, and (3) water isotopic geochemistry. Chemical and isotopic data were obtained from two sampling campaigns conducted in April (fall) and December (summer) of 2011 in 22 sampling locations, which included surface water and groundwater. The results obtained by each of the methodologies were mutually consistent and indicate high connectivity conditions. Additionally, the relative contribution by different sources was assessed through end-member mixing analysis, and for reaches of the river that showed gaining conditions, the contribution of groundwater inflow to stream discharge was estimated. It is suggested that this multi-method approach is useful for the characterization of surface-water-groundwater interactions, since it at least represents a suitable starting point for obtaining basic information on these relationships. Thus, it may become the base for further studies in arid and semi-arid basins facing water management challenges.