In order to monitor the eco-hydrological processes of the Heihe River basin, obtain spatially dense measures, determine the energy conversion rules and detailed characteristics of material migration within a small-scale system, a wireless sensor network (WSN) with a 4×4 grid was deployed in the basin. It is difficult to deploy and maintain a WSN system, especially in the study area of the Heihe River basin where harsh weather conditions and treacherous terrain can compromise the performance of such a system, while at the same time, high-energy efficiency, reliable delivery and high-quality measurements are required. To increase reliability under these conditions, protective and redundancy measures were utilised in the deployment. These nodes are now installed to collect data and transmit them through several repeaters to the base station in the experimental research establishment, where the data are automatically transmitted to the server in the establishment, and finally transferred to supercomputers in our institute through an optical fibre channel, thus achieving complete automated online data storage, analysis and real-time display. The monitoring of the Heihe River basin via WSN has now enriched field observation capabilities, and will create an e-Science application for eco-hydrological research.