The unique water systems of the Baroque monasteries are shown and rehabilitation of historic structures are analysed. The understanding of the original or older solution, its technical parameters and performance is the first step towards restoration. The monastery of Plasy (Pilsner region) was founded on aquiferous sediments. This indicated a very bold and unique way of founding on oak piles and raft. The whole system of the foundation is divided into individual parts, each providing specific purpose: water supply, control points, drainage galleries and ventilation system, but only together they form a functional unit. In the past the monastery has changed owners, disrupting the continuity of the maintenance and knowledge of the system. Water galleries critical to the stability of the building have been disconnected and galleries became clogged with sediment, many inappropriate interventions have been made. Due to the hard to reach parts of the water system, not all damage is yet fully identified. Tracking tests allowed a better understanding of the mutual interconnection of the different parts of the water system. There is an effort to understand the mutual synergy of the different parts. Chemical analyses of the water were carried out to determine the current state of pollution. The effectiveness of the repair was evaluated by measuring the internal microclimate. The installation of the copy of Baroque fountain, providing cold water spray does not deteriorate the indoor microclimate, but on the contrary slightly improves it. The rehabilitation of the ventilation has proved to be effective.