The first phase of the Taparura Project aimed at restoring the north coast of Sfax (Tunisia), highly polluted by phosphate industry and uncontrolled phosphogypsum dumping. Before restoration of the north coast of Sfax, we investigated the state of the ecosystem in related coastal waters. To establish the impact of the Taparura Project, we conducted a similar study both after restoration. To discriminate natural changes over time, we extended the study to the south coast of Sfax, submitted to the same industrial pressure but not yet restored. The present study, conducted in May 2010 at 36 stations (18 on each coast, north and south), covered the spatial distribution of the microbial assemblage, nutrients, and abiotic parameters by collecting seawater samples at the surface and the water–sediment interface. Results revealed a striking difference between the two coasts regarding pH, with strong acidification of seawater in the south, likely generated by industrial activity. Suspended matter was higher in the north than in the south. Flow cytometry analysis of ultraphytoplankton (<10 μm) resolved six groups (Prochlorococcus, Synechococcus, nanoeukaryotes and three distinct subgroups within picoeukaryotes). In addition to these autotrophic groups, two unknown groups were characterised on the south coast. Heterotrophic prokaryotes were resolved into three groups, labelled LNA (low nucleic acid content), HNA1 and HNA2 (high nucleic acid content). Prochloroccocus, pico-nano-microphytoplankton, heterotrophic prokaryotes and ciliates were more abundant in the north, whereas Synechococcus and unknown species were more abundant in the south where chl a concentration was also higher. The results show that restoration had positive effects on the microbial assemblage of the north coast; they also highlight the strong acidification still prevalent in the south that may be responsible for the lower development of most phytoplankton groups and the occurrence of unknown species. The case for restoration of the city’s south coast is also reinforced.