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This paper analyses the temporal dynamics of soil water balance components in a representative recharge area of the Sierra de Gador (Almeria, southeastern Spain) in two hydrological years. Two approaches are used to estimate daily potential recharge (PR): Approach 1 based on deriving PR from the water balance as the difference between measurements of rainfall (P) and actual evapotranspiration (E) obtained by eddy covariance; and Approach 2 with PR obtained from the dynamic pattern of the soil moisture (theta) recorded at two depths in the site’s thin soil (average 0.35 m thickess). For the hydrological year 2003/04, which was slightly drier than the 30-year average, E accounted for 64% of rainfall and occurred mainly in late spring and early summer. The PR estimated by Approach 1 was 181 +/- 18 mm year(-1) (36% of rainfall), suggesting an effective groundwater recharge in the study area. In the unusually dry hydrological year 2004/05, E was about 215 mm year-1, close to the annual rainfall input, and allowing very little (8 +/- 12 mm year-1) PR according to Approach 1. Estimation of PR based on Approach 2 resulted in PR rates lower than those found by Approach 1, because Approach 2 does not take into account the recharge that occurs through preferential flow pathways (cracks, joints and fissures) which were not monitored with the theta probes. Moreover, using Approach 2, the PR estimates differed widely depending on the time scale considered: with daily mean theta data, PR estimation was lower, especially in late spring, while theta data at 30 min resolution yielded a more reliable prediction of the fraction of total PR resulting from the downward movement of soil water by gravity.