Water Treatment Plants (WTPs) play a key role in assuring water availability to citizens and businesses. Long term availability of these plants is the interest of the asset manager of a WTP and can be influenced by maintenance strategies and modifications of the system. A WTP is characterized by a complex configuration and repairable, deteriorating assets. Currently, no method in the literature is known for modelling the long term availability of systems with these characteristics. This research introduces a two level hierarchical model: it deals with complexity at the system level and with repairable, deteriorating assets at the component level. At the component level the asset manager has to select between a condition based or failure event based model. A flowchart supports the decision making process for this choice. The result is a method which allows the asset manager to (1) learn about what key components affect long term availability of a WTP and (2) explore maintenance strategies and modifications to the WTP and their effect on long term availability.