The Swiss ATES pilot plant,SPEOS, is located in Lausanne near Lake Geneva. The installation consists of a large central well with a network of horizontal drains in each of two successive sandy aquifers. Water goes from one level to the other during the injection and production cycles.Slight changes in the chemistry of the aquifer have been observed, generally with a low impact. Scaling and clogging by calcium carbonate precipitation are the biggest problem. Many experiments have been performed to find a good solution. Different types of heat exchangers have been tested: tubular, plate, and fluidized bed. Several water treatment methods were also investigated: mechanical, electromagnetic conditioning and injection of chemicals. The fluidized bed heat exchanger is currently running in SPEOS. Continuous injection of HCl (hydrochloric acid) was an effective solution for scaling prevention but it resulted in an increase in chloride concentration and in corrosion of the equipment (including stainless steel). Therefore, a better solution must be chosen, possibly without the use of chemicals, which may lead to environmental impacts.Microbiological studies were performed to help understand the behaviour of the aquifer microflora to an increase in temperature and possible other changes provoked by the aquifer's exploitation as a thermal storage. Up to now, the hygienic quality of the water has not been altered. But some potentially pathogen microorganisms like Legionella may represent a biological hazard. Therefore, it is necessary to evaluate disinfection methods.