Diseases represent a major threat for the bivalve production industry. Their control relies on biosecurity measures to prevent their introduction and limit their spread. When maintained in hatcheries, nurseries and depuration centers, bivalves can become infected from the surrounding water and might release pathogens through wastewater effluents. A major effort was done in controlling the safety of bivalves for human consumption, but, on the other hand, information regarding the resistance of mollusc pathogens to water treatment is scarce. The effect of ultraviolet exposure was tested on two protozoan parasites of marine bivalves, the non-culturable parasite Bonamia ostreae and Perkinsus olseni culturable in DMEM/HAM´s medium. UV exposure experiments were carried out first at the bench scale and then, for P. olseni, at a larger scale mimicking depuration plants, hatcheries and nurseries conditions. At the bench scale, our study indicated that up to 40% of B. ostreae cells and 85% of P. olseni cells died 24 h and 21 days respectively after an exposure to 94 mJ/cm2 of UV-C. After 40 mJ/cm2 exposure, P. olseni density increased between 15 and 21 days of culture suggesting that the parasite is able to recover from low UV intensity exposure. At large scale, no signs of UV recovery were seen in P. olseni cultures, but, at lower intensity (216–244 mJ/cm2), 15% of the parasites remained alive 21 days post exposure. Finally, a minimum dose of 94 mJ/cm2 seems required to inhibit proliferation of parasites and 450 mJ/cm2 to completely kill all parasites. Taken this into account, a dose higher than 450 mJ/cm2 is suggested to properly treat water to avoid dispersion of bivalve protozoan parasites such as P. olseni.