The spatial and seasonal variability of the microphytoplankton and ciliates communities in relation to the environmental factors were studied in the southern coastal area of Sfax. Results revealed a striking difference between seasons regarding pH, with strong acidification in autumn generated by industrial activity. Spatial distribution of pH in autumn impacted the microorganisms in different ways: acidic stations to the south showed significant correlations with Cyanobacteria, dinoflagellates and loricate ciliates whereas higher pH values in spring (pH > 8) were linked to diatoms richness. The high availability of inorganic phosphate is associated with the high release of phosphate due to residue from a phosphate treatment manufacture along the coast; consequently, N/P ratios were low (1.34–13.43) suggesting nitrogen limitation. Microphytoplankton abundance shifted from dinoflagellates dominance in autumn to dominance of diatoms during winter and of Euglenophyceae in summer. Loricate ciliates accounted for the largest proportion of the ciliates community while aloricate ciliates were relatively scarce during all seasons. Variability of ciliate community appeared not directly linked to environmental conditions, but significant positive relationships between abundance of loricate ciliates and microphytoplankton suggest that these ciliates may feed on microphytoplankton.