This study examines the variability of in-pool temperatures in Imnavait Creek, a beaded arctic stream consisting of small pools connected by shallow chutes, for the purpose of predicting potential impacts of climate variations on the system. To better understand heat fate and transport through this system, the dominant heat sources and sinks creating and influencing thermal stratification within even the smallest and shallowest pools must be quantified. To do this, temperature data were collected vertically within the pool water column and surrounding bed sediments during stratified conditions. These temperature and other supporting data (e.g. instream flow, weather data, and bathymetry) were used to formulate and develop an instream temperature model that captures the site-specific processes occurring within the pools during summer low flow conditions. The model includes advective, air–water interface, and bed conduction fluxes, simplified vertical exchange between stratified pool layers, and attenuation of shortwave radiation within the water column. We present the model formulation, data collection methods used in support of model development and population, and the resulting model calibration and validation for one of the study pools. We also provide information regarding dominant heat sources and sinks and residence times of different layers within the stratified pool. We found that the dominant heat sources vary between stratified layers and that increases in thaw depths surrounding these pools due to possible climate changes can shift stratification, mixing, and instream storage dynamics, thereby influencing the fate and transport of heat and other constituents of interest (e.g. nutrients). Copyright © 2011 John Wiley & Sons, Ltd.