Market penetration of renewable energy sources, such as geothermal energy, could be promoted even by small cost reductions, achieved through improved development design. This paper deals with optimization of the exploitation system of a low enthalpy geothermal aquifer, by means of the method of genetic algorithms, which has been successfully used in similar problems of groundwater resources management. With respect to water flow, the aquifer consists of two zones of different transmissivities, while from the thermal point of view it may bear any number of zones with different temperatures. The optimization process comprises the annual pumping cost of the required flow and the amortization cost of the pipe network, which carries the hot water from the wells to a central water tank, situated at the border of the geothermal field. Results show that application of the proposed methodology allows better planning of low enthalpy geothermal heating systems, which may be crucial in cases of marginal financial viability. (C) 2009 Elsevier Ltd. All rights reserved.