A water-flow window consists of two glass panes making up a chamber in which a water layer flows in a controlled way. Such windows may be considered as Building-Integrated Solar Thermal (BIST) collectors, and could assist to incorporate renewable energy systems in buildings, improving their energy efficiency, especially when they are properly managed by a control system. Despite the need of an automatic controller for this kind of window and the advantages of microprocessor-based control for solar systems, only differential controllers have been described. A novel controller based on an inexpensive open source microcontroller board has been designed, built, programmed and installed in an experimental prototype water-flow window. The proposed data acquisition and control system, the code sequence steps, a model algorithm, and a comparison between the data collected by the system and a commercial datalogger are presented. The advantages of using an open source board for the proposed control system are analysed and the benefits of using a control system based on a microcontroller are discussed. (C) 2016 Elsevier Ltd. All rights reserved.