The vertical and temporal dynamics of total picoplankton, heterotrophic nanoflagellates and ciliates were monitored monthly from May 2002 to April 2003, along with environmental parameters, in Lake Faro, a meromictic coastal basin characterized by a permanently anoxic monimolimnion and sulfide-rich bottom waters. A two-layer discrimination was delineated in the water column of the lake, based on the correlations between environmental and biological descriptors and on the ciliated protozoa community composition. The latter showed a clear zonation pattern along the water column with two main recognizable facies: a superficial and a deep one. Choreotrichida and Strombidiida dominated the upper facies nearly throughout the study period, while Tintinnida were only found in summer months. The mixotrophic cyclotrichid Myrionecta rubra was also frequently observed in the upper facies. Typical of the deep facies was the occurrence of Pleuronematida (Cyclidium sp.) and of flagellates of the order Cryptomonadida (Chilomonas sp.), which were the main potential picoplankton grazers during a summer bloom of photosynthetic sulfur bacteria. Sporadic inputs of Levantine Intermediate Waters (LIW) from the upwelling system of the Straits of Messina, although limited to the mixolimnion, clearly affected the physical and chemical environment, as well as the microbial biomass and the ciliated protozoa assemblage composition, all along the water column of the lake, suggesting that meromictic basins, although strongly stratified, may experience perturbation effects from the surface down to the bottom, with important consequences on their biogeochemical cycles and on their ecology.