Abstract. The water balance of the mesocenozoic aquifers of the Algarve, in the south of Portugal has traditionally been estimated considering only direct ("autogenic") recharge from rainfall occurring in the area of the aquifers. Little importance has been attributed to so-called allogenic recharge, originating from streambed infiltration from runoff generated outside the aquifers, particularly in the Palaeozoic rocks to the north where runoff is high. The Querença-Silves (QS) aquifer is the most important aquifer of the region both for irrigation and public water supply. Several important and sensitive surface/groundwater ecotones and associated groundwater dependent ecosystems exist at the springs of the natural discharge areas of the aquifer system. A numerical flow model has been in constant development over the last few years and currently is able to reproduce the aquifer's responses to estimated direct recharge and abstraction for the years 2001-2010. However, recharge calculations for the model do not take into account allogenic recharge infiltration along influent reaches of streams. The quantification of allogenic recharge may further improve the assessment of water availability and exploitation risks. In this paper an attempt is made to quantify the average annual contribution of allogenic recharge to the QS aquifer, based on monitoring data of the principal water courses that cross the aquifer system. Significant uncertainties related to surface runoff generated within the aquifer area, as well as areal recharge were identified and the consequences for the optimization of spatial distribution of transmissivity in the groundwater flow model are also addressed.

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