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Water temperature is a key physical habitat determinant in lotic ecosystems as it influences many physical, chemical, and biological properties of rivers. Hence, a good understanding of the thermal regime of rivers and river heat fluxes is essential for effective management of water and fisheries resources. This study dealt with the modelling of river water temperature using a deterministic model. This model calculated the different heat fluxes at the water surface and from the streambed using different hydrometeorological conditions. The water temperature model was applied on two watercourses of different sizes and thermal characteristics, but within a similar meteorological region, namely, the Little Southwest Miramichi River and Catamaran Brook (New Brunswick, Canada). The model was also applied using microclimate data, i.e. meteorological conditions within the river environment (1–2 m above the water surface), for a better estimation of river heat fluxes. Water temperatures at different depths within the riverbed were also used to estimate the streambed heat fluxes. Results showed that microclimate data were essential to get accurate estimates of the surface heat fluxes. Results also showed that for larger river systems, the surface heat fluxes were generally the dominant component of the heat budget with a correspondingly smaller contribution from the streambed. As watercourses became smaller and groundwater contribution more significant, the streambed contribution became important. For instance, approximately 80% of the heat fluxes occurred at the surface for Catamaran Brook (20% from the streambed) whereas the Little Southwest Miramichi River showed values closer to 90% (10% from the streambed). As was reported in previous studies, the solar radiation input dominated the contribution to the heat gain at 63% for Catamaran Brook and 89% for Little Southwest Miramichi River. Copyright © 2011 John Wiley & Sons, Ltd.