The use of simulation is a scientific-recognized way of studying biogeochemical cycles. That assumption is even more relevant when the study scope involves one or more disturbances: in that case, simulation helps students gain insight into the response dynamics of the respective biogeochemical cycle. The development of simulation tools for high school and undergraduate courses did not progress much for the last couple of decades, despite of the advances in computer science. Trying to fill in that gap, this paper presents the BCS (Biogeochemical Cycles Simulator) freeware, an up-to-dated choice for older simulators. The BCS is a light-weighted, user-friendly, Windows®-based simulator, whose results are in accordance with two former simulation tools. In fact, using the sulfur biogeochemical cycle as an example, the simulation results from two sequential disturbances were compared with those of the former tools: the sum of relative errors between the three tools was never greater than 2.7%. The major improvements made include: a friendly graphical user interface, unlimited number of reservoirs, direct input of mass fluxes, multi-disturbance assessment, and fully customizable plots. The BCS has been used in case studies, in a Biogeochemical Cycles course of a B.S. in Chemistry at the University of São Paulo, Brazil. One can observe that simulation helped students to develop decision-making and group-working skills, as well as enhanced data interpretation. Moreover, the students were able to recognize how even small disturbances can cause short- and long-term negative impacts on biogeochemical cycles.