River water temperature is a very important variable in ecological studies, especially for the management of fisheries and aquatic resources. Temperature can impact on fish distribution, growth, mortality and community dynamics. River evaporation has been identified as an important heat loss and a key process in the thermal regime of rivers. However, its quantification remains a challenge, mainly because of the difficulty of making direct measurements. The objectives of this study were to characterize the evaporative heat flux at different scales (brook vs river) and to improve the estimation of the evaporative heat flux in a stream temperature model at the hourly timescale. Using a mass balance approach with floating minipans, we measured river evaporation at an hourly timescale in a medium‐sized river (Little Southwest Miramichi) and a small brook (Catamaran Brook) in New Brunswick, Canada. With these direct measurements of evaporation, we developed mass transfer equations to estimate hourly evaporation rates from microclimate conditions measured 2 m above the stream. During the summer 2012, river evaporation was more important for the medium‐sized river with a mean daily evaporation rate of 3.0 mm day−1 in the Little Southwest Miramichi River compared with that of 1.0 mm day−1 in Catamaran Brook. Evaporation was the main heat loss mechanism in the two studied streams and was responsible for 42% of heat losses in the Little Southwest Miramichi River and 34% of heat losses in Catamaran Brook during the summer. Copyright © 2013 John Wiley & Sons, Ltd.