To obtain the fullest picture of geothermal systems, it is necessary to integrate different types of data, e.g., surface electromagnetic surveys, lithology, geochemistry and temperature logs. Here, by joint modelling a multi-channel dataset we quantify the spatial distribution of heat transfer through the hydrothermally-altered, impermeable smectite layer that has developed atop the Wairākei-Tauhara system, New Zealand. Our approach involves first constraining magnetotelluric inversion models with methylene blue analysis (an indicator of conductive clay) and mapping these onto temperature and lithology data from geothermal wells. Then, one-dimensional models are fitted to the temperature data to estimate heat flux variations across the field. As a result, we have been able to map the primary seal that insulates the geothermal reservoir and estimate the heat flow of the system. The approach could be applied in geothermal provinces around the world with implications for sustainable resource management and our understanding of these magmatic systems.