This paper presents the results of assessment of the protozoan Cryptosporidium spp. presence in the Mediterranean mussels (Mytilus galloprovincialis) exposed to anthropogenic influence, as well as the efficiency of purification of the bacterium Escherichia coli from mussels placed in the experimental purification system of the Institute of oceanography and Fisheries, Split. Analysed samples collected from the farming site Stipan Jaz in Marina close to Trogir were placed in plastic nets (pergolas) and left for two days at the marine location exposed to the anthropogenic source of microbiological contamination. Cryptosporidium spp. presence in the mussels showed negative results, which could have resulted from a variety of factors (low concentration or total absence of oocysts in the water column, reduction of oocysts due to freshwater flow, chemical and physical factors). In contrast, the concentration of E. coli bacteria and the efficiency of the treatment gave the expected results; the former was high in untreated mussels placed in the purification treatment system, indicating towards a significant microbiological contamination of the location under anthropogenic influence, and the capability of mussels to accumulate E. coli. Purification results showed strong decrease in E. coli levels in the first 12 hours of purification, after which a slow stagnation i.e. slower decrease in E. coli levels followed, after 24 and 48 hours of purification. Also, it has been noted that the concentration of E. coli after 48 hours has been reduced to the levels lower than the lowest permitted concentration for the farming site A (≤ 230 E. coli/100 g tissue and liquor). Based on this, it can be concluded that in specific conditions Cryptosporidium spp. does not represent a risk for human infection, while the applied purification process enables successful clearance of E. coli from the mussels.