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Background: The COVID-19 pandemic has disrupted global daily life, including the world of elite athletes. This paper examines the multifaceted impact the COVID-19 pandemic had on elite swimmers and water polo athletes, specifically their mental health, their concerns over the virus, their intentions of getting vaccinated, and sleep disturbances that they may have faced. Methods: We conducted a cross-sectional study on elite swimmers and water polo players, using an anonymous questionnaire. Results: A total of 200 elite athletes participated. The majority of the participants reported a negative impact on their mental health, screened positive for insomnia (n = 107 (53.5%), with females (n = 101; 57.7%), swimmers (n = 100, 66.7%), and university students (n = 71, 71.7%) being more vulnerable (p < 0.001). Concerns about contracting the disease especially during important training or tournament periods and potential career disruption also affected their psychological well-being. While the majority (75%) had the intention of getting vaccinated, an alarming percentage was yet uncertain over its decision. Conclusions: This study highlights the significant psychological distress faced by elite aquatic athletes during the pandemic. It emphasizes the difficulties faced by elite swimmers and water polo athletes and determines not only the importance of addressing the vaccination intentions of athletes, but also how critical it is to confront the challenges they face both for their personal health and for the restoration of world sports to their pre-pandemic state. More large-scale studies are required to inform policies targeted at minimizing disruption to the athletes' career, provision of information on preventive measures and vaccination, and improvement in psychological well-being in case of similar major public health issues in the future. Additionally, this study calls for further research to explore the unique challenges faced by aquatic athletes, such as those related to their training environments and fear of contagion, to better support them in future public health crises. [ABSTRACT FROM AUTHOR]