Groundwater-surface water (GW-SW) interactions cover a broad range of hydrogeological and biological processes and are controlled by natural and anthropogenic factors at various spatio-temporal scales, from watershed to hyporheic/hypolentic zone. Understanding these processes is vital in the protection of groundwater-dependent ecosystems (GDEs) increasingly required in water resources legislation across the world. The use of environmental tracers and indicators that are relevant simultaneously for groundwater, surface water and biocenoses-biotope interactions constitutes a powerful tool to succeed in the management task. However, tracer type must be chosen according to the scale of interest and tracer use thus requires a good conceptual understanding of the processes to be evaluated. This paper reviews various GW-SW interaction processes and their drivers and, based on available knowledge, systemises application of conservative tracers and semi-conservative and reactive environmental indicators at different spatial scales. Biocenoses-biotopes relationships are viewed as a possible transition tool between scales. Relation between principal application of the environmental tracers and indicators, examples and guidelines are further proposed for examining GW-SW interactions from a hydrogeological and biological point of view by demonstrating the usability of the tracers/indicators and providing recommendations for the scientific community and decision makers.