Meta-Goal Programming (MGP) is a simultaneous cognitive evaluation of the degree of achievements for original decision goals considered in a GP model. However, in most real-world situations, environmental coefficients and related parameters are not easily available. In such a situation, the decision-maker must consider various conflicting targets in a framework of uncertain aspiration levels at the same time. On the other side, Interval Programming (IP) is a method used to increase the range of available decision-maker preference structures in GP. In the perspective of solving the conflicts between agriculture and water use towards sustainability, this paper proposes an Interval Meta-Goal Programming Model (IMGPM) dealing with imprecision in data that covers interval coefficients, target intervals, and interval bounds of meta-goals. This novel methodology has been tested in a study area in Iran to validate its added value in solving conflicting uses of natural resources by economic sectors. This integration together with its application for sustainable optimal cropping patterns (agroecosystem planning) represents a novelty in the field of ecological modeling. The management solutions of our method in terms of land allocation are different from those in Sen and Pal (2013) model. In the case of Iran, many socio-ecological-economic strategies and policies should be necessary for improving the agricultural sector. More specifically, on the basis of rainfall amounts and spatial patterns, this approach can represent a decision-support system able to define strategies for additional water storage useful to support crop production. Furthermore, the availability of water together with the sustainable use of fertilizers can mitigate the risk of land degradation, guaranteeing people employment, food security, and economic profits. Although the present methodology seems to solve the problem of multi-goals decision-making, the inclusion of spatial relationships is able to introduce dependencies between the management of land use in adjacent areas, making the present approach nearer to real-world functioning.