Water scarcity has a significant impact on agricultural productivity, and it usually constitutes the main criterion for the continuation of agricultural activity. Cyprus agri-sector faces increasing challenges since water resources are very limited and particularly susceptible to climate change. As total profit highly depends on cultivation patterns, the present study aims to define the optimal pattern of agricultural crops in Cyprus. A Linear Programming Model is set up to maximize the net profit of annual and permanent crops. As for the constraints, these include limitations on land and water availability under four different Scenarios, provided that production secures current consumption of (1) domestic products, (2) domestic and imported products, (3) domestic products but under a 40% decrease in water availability and (4) domestic products but limited to only traditional, tropical and subtropical crops, under a 40% decrease in water availability. The results indicate that when using an optimal cultivation pattern, economic benefit increases compared to 120%, 62, 20, and 48%, based on Scenarios 1, 2, 3 and 4, respectively. Furthermore, the results are considered useful and directly applicable to policy makers to redesign their strategy in light of water scarcity.