The COVID-19 pandemic has left behind mental health issues like anxiety, depression, and sleep disorders among survivors. This study assessed the efficacy of spa therapy in enhancing psychological well-being and sleep quality in individuals with chronic arthro-rheumatic, respiratory, and otorhinolaryngological diseases, including COVID-19 recoverees. Our prospective observational study included 144 Caucasian subjects from three Italian spas who underwent a 2-week spa therapy cycle, involving balneotherapy and/or inhalation treatments. Symptoms were assessed with the Visual Analogue Scale (VAS), psychological well-being with Depression Anxiety Stress Scales-21 items (DASS-21), and sleep quality with the Insomnia Severity Index (ISI). Significant reductions in VAS scores for arthro-rheumatic, respiratory, and otorhinolaryngological symptoms were observed after spa therapy, as well as for DASS-21 and ISI scores for sleep quality, transitioning to less severe insomnia categories. Females had more pronounced improvements in DASS-21 scores and sleep quality. Subjects with and without prior SARS-CoV-2 infection experienced significant reductions in anxiety, depression, and stress, with more pronounced improvements in those without prior infection. COVID-19 survivors also showed significant ISI score improvements. Spa therapy is a promising complementary treatment for improving mental health and sleep quality in chronic disease patients, including COVID-19 survivors.