The present chapter provides a brief explanation on some aspects involved in the development of models and mathematical-modelling simulations, to show their benefits to the decision-making process in the environmental impact assessment of agriculture. Aspects concerning the agroecosystems were also presented toward the sustainability of Brazilian agricultural production systems. Some applications which have been developed in Brazil were pointed out, as well as a specific case study conducted at the Guarani aquifer recharge area located in Ribeirão Preto, São Paulo state, in order to show the influence of input data on the results provided by CMLS94 simulator.