Traditionally airport systems have been studied using a decomposition approach in which the differentelements of the system are studied independently. For example TMA operations have been studied in such a way that theairport plays the role of just the end or starting point of the traffic involved. On the other hand the ground systemcomposed by the runway and taxi network has been also studied independently in order to maximize its capacity.Furthermore, these independent approaches suggest that either the ground system or the TMA space have sufficientcapacity to accommodate the traffic involved. Until recently scientific community has put attention in developing modelsand techniques that study the system using holistic approaches in order to understand the cause and effect relationships ofthe integral system and then come up with approaches that provide more robust and efficient solutions than the ones thatcan be achieved through individual analysis. This paper presents a methodology that includes different elements fromboth systems such as TMA topology, runway, taxi networks, and ground handling operations that first aims at identifying the elements that hinder the smooth process of the air traffic and second it optimizes the system through an efficient management of the resources that play an important role in the performance of the system. The methodology uses evaluation techniques such as simulation together with optimization techniques for the efficient management of the resources of the system. The methodology is composed by different analytic stages, the first stage identifies the parameters that affect the system the most. The latter is achieved through the development of a simulation model of an integral airport system (Ground Operations + TMA). The results obtained from this phase will be used in the second stage to parameterize the optimization model of the integral system.The paper presents the results of the evaluative stage in which the main factors are identified and analyzed. In the second stage of the methodology the identified factors will be used as decision variables for optimizing the managerial problem. The methodology has been implemented for studying the situation of Lelystad Airport in the Netherlands.