This paper studies the environmental efficiency of wheat crops in the different regions of Spain where it is grown. Both rainfed and irrigated wheat cropping systems are considered. Excepting irrigation water consumption, the two groups of observations share the same inputs (namely, N Fertilizers and Non-renewable energy) and outputs (namely, Yield, soil organic carbon, NH3 emissions, NO3− leaching and Global Warming Potential). The three undesirable outputs considered are handled using the transformation method. Given the stochastic character of the variables, a Chance Constrained DEA approach is proposed. A non-radial directional distance function (DDF) model is used. The proposed approach provides deterministic efficiency, stochastic targets and reference units. The two groups of observations are compared using a metafrontier approach and the corresponding technology gap ratios are computed. For each group of observations, the results have identified the best practice regions and those where environmental efficiency improvements are needed.