Background: Balneotherapy and hydrotherapy offer interesting treatment alternatives and are commonly used as additional interventions in the management of musculoskeletal disorders and pain management. Therefore, the aim of this study was to assess the effect of balneotherapy on musculoskeletal disorder pain and its perceived improvement among users of hot spring water in Southern Ethiopia. Methods: A single-arm cohort study and convenient sampling method were used to select 1337 study participants from four hot springs in Southern Ethiopia. A structured questionnaire, a physical examination, and laboratory blood tests were used to collect data. Data were entered using Epi data and transferred to SPSS 25 for cleaning and analysis. Descriptive analysiswas made. Results: Atotalof 1279participantswere included in thestudy, giving aresponserate of 96%. The majority of these patients have multiple health problems. Of all, 1137 (88.9%) of the patients were visiting the hot springsforjointpainfollowedbymusclepain669(52.2).Outofallcasesofjointpain,132(11.6%)wereclinicallydiagnosedwith rheumatoid arthritis, and 5.3% were confirmed as having the disease based on a laboratory test. Of the total number of study participants, 1064 (83.2%) reported complete relief from the complaints they had at the start of the bath. Conclusions: Hot spring baths for three and more days have significant therapeutic effects on patients with musculoskeletal disorders, including rheumatoidarthritis.Physicianswhoarecurrentlyworkingintheareaofdiagnosisandtreatmentofpatientsingovernmentand public facilities of the southern region should consider hot spring bath treatment for those patients with complaints of musculoskeletal pain, nonspecific arthritis, and rheumatoid arthritis. A hot spring bath is beneficial for everyone because it is a natural treatment with few side effects and a low cost.