A hierarchical sampling design was used during two seasons (spring (May) and summer (August) 2006). Using this design, three regions of the Kerkennah Islands (Tunisia) were analyzed for the distribution of microalgal, protozoan and metazoan assemblages in two different habitats: (1) the water column; and (2) on Posidonia oceanica (L.) Delile (P. oceanica) leaves in shallow meadows. A total of 85 species were obtained. In particular, the diatom family Naviculacea consistently dominated (both numerically and in their diversity) the micro-algae in all regions for the two seasons of the study and in both habitats. In the Chergui region, which is the closest area to a source of impact, fast growing centric diatoms (such as Thalassionema, Rhizosolenia, Striatella, and Skeletonema) were identified as indicators of high organic matter and nutrient enrichment in water bodies. Protozoan and metazoan species abundance in the different regions indicate a non-random spatial and temporal distribution of the epiphytic organisms on leaves of P. oceanica that correlated with phytoplankton. The results also indicate that (1) the abundance of micro- and macroorganisms in the three regions were higher on P. oceanica leaves than in the water column for the two seasons; (2) environmental factors such as currents and tide influenced assemblages; and (3) the highest abundance was due to direct exposure to the polluted coast of Sfax and the effect of tidal asymmetries generating nutrient-rich inputs from the city.