Greece is a country where the main way of waste disposal is landfilling. In the Prefecture Ilia, a region that is situated in the South of Greece, the waste management policy does not seem to fulfill adequately the requirements that are set by the EU legislation or to meet the primary goals of waste management, since the common practice is uncontrolled dumping. In order to support more efficient future strategies an alternative waste management system is presented and quantitatively assessed by means of Material Flow Analysis (MFA). This alternative is based on two central EU Directives, the Waste Framework Directive and the Landfill of Waste Directive, and Greek legislation, takes into consideration the waste generation of the region and the present waste treatment infrastructure and introduces the concepts thermal treatment, anaerobic digestion and recycling. By changing the recycling rates two sub-scenarios are formed, evaluated and compared to the status quo. The results show that a waste management system that embraces incineration, anaerobic digestion as well as improved landfilling complies with the EU legislation and attains better the goals of waste management. Following this, a rough economic assessment of the suggested options and of the current waste management system takes place. According to this assessment, the costs of disposing waste in uncontrolled dumpsites are the lowest while the costs for changing the waste management landscape are considerable. However, the picture changes significantly in case the country has to pay fines to the EU for the illegal dumpsites of the region. This study intends to underline the environmental benefits that come from setting up a completely new waste management system, to indicate how this system, at regional level, could contribute in complying better with the EU Directives and to express the idea that reforming the waste management system cannot be avoided even if it seems expensive, considering that the economic penalties for the uncontrolled dumpsites that function at present are at the gates.