This present work studies the prediction of water resource quantity in Cyprus by using the mathematical technique called the Markov chains of the fuzzy states (MCFS) prediction method. This region is considered as a poor water country in Europe with a semi-arid climate that also has a frequent occurrence of drought and limited water resources that are mainly dependent on rainfall. Cyprus is suffering from unevenly distributed rainfall and small catchments, where extreme drought events are suspected due to climate change. The water policy in Cyprus is based on two pillars: sustainable development of water resources and water demand management. Around 1970 changes in the rainfall pattern in addition to population growth led to critical situations in many aquifers, which deteriorated due to the intrusion of seawater intrusion into the aquifer. Hence, the estimation of water resource values and water consumption for the following decades is important to implement effective management plants. By collecting and analyzing 100 years of standardized precipitation index data the future expected precipitation probabilities of the island of Cyprus were estimated using Markov chains (MC) and MCFS analysis. For this purpose, the inter-state transition probability matrix of the system has been determined and long-term equilibrium vectors have been calculated to determine the stability of the system. This study shows that the use of the MCFS gives more sensitive results for the prediction of future precipitation than the classical MC model.