This paper presents a model and simulations, which was built with a System Dynamics methodology applied to waste management in the bioethanol supply chain in Colombia. The stages of the supply chain used were cane planting, production and the distribution process. The residues taken into account were bagasse and vinasse. Moreover, four simulation scenarios were performed in which the values of variables modified management strategies. The installed bioethanol production capacity was increased to observe the evolution of increased waste generation evaluated. The initial conditions for the simulation were modified to represent a production of about 2,500,000 liters / day. This leads to an increased generation of vinasse of over 400 million liters on average in a month and around more than 1 million tones of bagasse. The results are used to estimate the impact of management strategies on the amount of waste generated in the production of bioethanol.