Globally, around 1 in 10 children aged 0–17 years have moderate-to-severe disabilities. The aquatic environment provides hydrostatic and hydrodynamic characteristics that make exercise and therapy feasible for children and adolescents with disabilities. The objective of this scoping review is to understand the extent and type of evidence in relation to the use of aquatic therapy in children and adolescents with disabilities. The eligibility criteria were as follows: participants—children and/or adolescents with disabilities aged from 6 to 18 years old; concept—aquatic therapy interventions; context—any available setting. The databases searched included MEDLINE, CINAHL, EMBASE, PsycINFO, AMED, Eric, Scopus, Web of Science, Epistemonikos, and one register, Cochrane Central Register of Controlled Trials. In total, 52 reports met the inclusion criteria. Most of the studies included children/adolescents with autism spectrum disorder (ASD; 46.7%)—442 participants in 21 studies in total. The majority of interventions were based on aquatic exercise (35%). Most often, interventions were conducted for 8 weeks, with 2 sessions a week lasting 60 min. The most common type of intervention for children and adolescents with ASD and Down syndrome was swimming. Participants with attention deficit hyperactivity disorder, neuromuscular disorders, and cerebral palsy were more often treated with aquatic exercises. This scoping review could guide practitioners, clinicians, and researchers on what type, setting, and content of aquatic therapy interventions, including exercise types, intervention duration, number of sessions, frequency, facility, and provider, are used with children and adolescents with disabilities.