The problem of biological invasions attributed to ballast water release is an ongoing problem that threatens ecosystems and human health. Ultraviolet (UV) radiation has been increasingly used for ballast water treatment mainly due to the advantages of short contact time and minimized harmful disinfection by products. In this study, the impact of salinity on the inactivation of Vibrio cholerae (NCTC 7253) was examined, and comparison of inactivation level and disinfection kinetics after medium-pressure (MP) (1 kW) and low-pressure (LP) (10 W) UV irradiation was made. MP UV exposure resulted in higher inactivation efficacy against V. cholerae than LP UV exposure especially at lower UV doses (≤3 mJ cm−2) and salinity had a negative impact on both MP and LP UV disinfection, especially at higher UV doses (≥3 mJ cm−2 for MP and ≥4 mJ cm−2 for LP). To understand the mechanisms of salinity effect on V. cholerae, the enzyme-linked immunosorbent assay (ELISA) was employed to determine the number of cyclobutane pyrimidine dimers (CPDs), one major type of DNA damage. No significant effects of salinity were found at the CPDs level except for 3% artificial seawater after LP UV exposure case. It is imperative that site-specific conditions of salinity be taken into account in the design of UV reactors to treat V. cholerae and other species.