Research capacities are developed scientific skills that enable universities to accomplish the dissemination of high-quality scientific knowledge. Nowadays, the modeling of their dynamics is one of the most important concerns for the stakeholders related to the scientific activity, including university managers, private sector and government. In this context, the present article aims to approach the issue of modeling the capacities of the Universities’ research systems, presenting Systems Dynamics as an effective methodological tool for the treatment of data contained in intellectual capital indicators, allowing to estimate parameters, conditions and scenarios. The main contribution lays on the modeling and simulations accomplished for several scenarios, which display the critical variables and the more sensitive ones when building or strengthening research capacities. The establishment of parameters through regression techniques allowed to more accurately model the dynamics of the variables. This is an interesting contribution in terms of the accuracy of the simulations that later might be used to propose and carry out changes related to the management of the universities research. Future research with alternative modeling for social systems will allow to broaden the scope of the study