Aquatic ecosystems represent one of the largest reservoirs of phytoplankton accounting for most of the primary production of the Earth. The Lake Massaciuccoli located in Tuscany (Italy) is one of the largest swamps that in ancient times entirely covered the Versilia coastal plain. Despite its peculiar features, especially the eutrophic characteristics, its native microalgal consortia have never been explored up to now. In this work, we isolated and described four autochthonous microalgal strains from different sites in the lake (FB, Idr, CL_Sc, and CL_Ch); the four microalgal strains were identified within the Chlorella sorokiniana clade. We exposed them to ten of the most common or emerging environmental contaminants in order to describe their preliminary response to the tested substances: five metals (As, Fe, Ni, Cu, and Zn), two herbicides (Metolachlor and Sethoxydim), two antibiotics (Ciprofloxacin and Benzylpenicillin) and a non-steroidal anti-inflammatory drug (Ibuprofen). Physiological response of the strains highlighted intraspecific differences; strain CL_Sc was the most tolerant in presence of metals while strain Idr was the most sensitive. All strains were sensitive to sethoxydim and tolerant to metolachlor at all the tested concentrations. Strains FB and Idr were the most sensitive in presence of Ibuprofen while strain CL_Ch was the most sensitive to the highest Benzylpenicillin concentration. Resistance pattern of strain Idr somehow reflects both the phylogenetic and the geographic "isolation" from all other three strains. Finally, optical microscope observation confirmed some differences also in the microalgae morphological aspect. Overall, all the strains showed interesting responses in presence of high concentrations of the tested substances, representing putative interesting candidates for water remediation in wastewater treatment plants.