Natural conditions and traditions of agriculture production are challenging by sustainable development in Slovakia. The significant portion of arable land is devoted to the cultivation of crops, especially cereals, feed crops and industry crop. There is a high representation of mountains areas in country, therefore the fertile lowlands in west-south and east part are the primary locations of almost all agricultural production. The main objective of this work is to integrate the bio-physical crop data on yields with the economic data enabling to calculate net returns, in order to identify alternative costs of agricultural management practices for cultivation of 13 most important crops in selected west-south regions of Slovakia. We use bottom up optimization model which is based on linear programming. Management practices are differentiated according to nutrient input and irrigation application in order to evaluate yields as well as environmental factor – water use efficiency. Results suggest that in terms of net returns the management practices with high and medium nutrient input without irrigation are the most profitable but can represent a potential environmental pressure for soil. Such kind of optimization targets to create a better condition to reach environmental and economic balance of crop production.