This study deals with the use of a multivariate analysis method in order to understand the functioning of the Bizerte lagoon ecosystem. A set of hydrobiological parameters was collected during 10 monthly campaigns in 2004. A variant of the EOF (Empirical Orthogonal Function) technique is used to examine hydrobiological variability modes in this lagoon. The permanent features characterising the lagoon are obtained by applying the EOF technique to data after removing the annual cycle. Two major modes were obtained. The first one shows a contrast between the northern sector of the lagoon, influenced by the Mediterranean Sea, and the southern one influenced by continental waters. This mode is mostly prominent for temperature and salinity. The second mode shows a contrast between shallow waters along the coastal zones and the deep central area of the lagoon. This contrast is more pronounced towards the southwestern edge of the lagoon, a region of important freshwater input from the Tinja channel, which drifts towards the downstream area of Menzel Bourguiba. This second mode may also correspond to northward water circulation under southerly wind blowing frequently in summer. The spatial and temporal variability in the lagoon is highlighted by applying the EOF to the raw data without removing the annual cycle. A weight series is obtained for each variable by extracting the corresponding data and then projecting them on the corresponding eigenvector. Using this technique, only one mode was found dominant with more than 52% of the total variance. It was also found that the north-south contrast of temperature, salinity and phosphorous and the coast-centre contrast of Chlorophyll a are enhanced in summer. Other variables such as ammonia and nitrate also show significant annual cycles but with local patterns. (C) 2008 Elsevier Ltd. All rights reserved.