Interactions between groundwater and surface water play a fundamental role in the functioning of riparian ecosystems. In the context of sustainable river basin management it is crucial to understand and quantify exchange processes between groundwater and surface water. Numerous well-known methods exist for parameter estimation and process identification in aquifers and surface waters. Only in recent years has the transition zone become a subject of major research interest; thus, the need has evolved for appropriate methods applicable in this zone. This article provides an overview of the methods that are currently applied and described in the literature for estimating fluxes at the groundwater – surface water interface. Considerations for choosing appropriate methods are given including spatial and temporal scales, uncertainties, and limitations in application. It is concluded that a multi-scale approach combining multiple measuring methods may considerably constrain estimates of fluxes between groundwater and surface water.