Stream confluences are important hotspots of aquatic ecological processes. Water mixing dynamics at stream confluences influence physio-chemical characteristics of the stream as well as sediment mobilisation and pollutant dispersal. In this study, we investigated the potential for handheld thermal infrared (TIR) imagery to provide rapid information on stream water mixing dynamics at small scales. In-situ visualisation of water mixing patterns can help reduce analytical errors related to stream water sampling locations and improve our understanding of how confluences and tributaries influence aquatic ecological communities. We compared TIR-inferred stream temperature distributions with water electrical conductivity and temperature (measured with a submerged probe) data from cross-channel transects. We show that the use of a portable TIR camera can enhance the visualisation of mixing dynamics taking place at stream confluences, identify the location of the mixing front between two different water sources and the degree of mixing. Interpretation of handheld TIR observations also provided information on how stream morphology and discharge can influence mixing dynamics in small streams. Overall, this study shows that TIR imagery is a valuable support technique for eco-hydrological investigation at small stream confluences.