Aquatic therapy improves motor skills of persons with Autism Spectrum Disorders (ASD), but its usefulness for treating functional difficulties needs to be verified yet. We tested effectiveness of a multisystem aquatic therapy on behavioural, emotional, social and swimming skills of children with ASD. Multisystem aquatic therapy was divided in three phases (emotional adaptation, swimming adaptation and social integration) implemented in a 10-months-programme. At post-treatment, the aquatic therapy group showed significant improvements relative to controls on functional adaptation (Vineland Adaptive Behavior Scales), emotional response, adaptation to change and on activity level (Childhood Autism Rating Scale). Swimming skills learning was also demonstrated. Multisystem aquatic therapy is useful for ameliorating functional impairments of children with ASD, going well beyond a swimming training.