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This study aims to assess the physico-chemical variability of the Alqueva reservoir during its initial filling period. The dataset consists of analytical results from an 11 month survey (Mar 2003-Jan 2004) conducted in the water body, at three levels of depth in the several tributaries and in the discharge section. 21 parameters were monitored on a monthly base, in order to understand the temporal and spatial variability. Another goal of this work was to use a multivariate statistical approach to help understand the relationships between water quality parameters, to group zones according to their similarities and to distinguish between wet and dry season conditions. FA/PCA needs 6 VF/PC to point out 74 % in the wet season, and 7 VF/PC to explain 78.6 % of variance in the dry season. FA/PCA allows grouping the selected parameters according to common features. As a result, mineral content is indicated as the principal source of variability in the wet season, while oxygenation plays the main role in the dry season. DA renders an important data reduction using 10 parameters to provide 93.2 % right assignations during temporal analysis. DA assigns temporal variability to the consequences of water balance on ambient salinities, to stratification influences and to surface runoff. Also, it uses only 4 parameters to yield 71.3 % right assignations during the spatial analysis in the dry season. Conductivity declines in the lacustrine zone, while CBO5, pH and Temperature vary principally in the vertical sense. However, such a spatial pattern is not static. It can become either more defined during the dry season, or less evident during the expansion of the lotic conditions in the rainy period (late spring and summer). Seasonal processes of stratification/mixture determine the temporal changes in the lacustrine zone. The system seems to be affected by periodic pulses of modifications produced by intensive rains and drought. Thus, limnological understanding of these questions is a prerequisite for making wise judgments about reservoir management.