A variety of aquatic training regimens have been found to be beneficial for individuals with autism spectrum disorders (ASD) in multiple domains. This study investigated and compared the efficacy of two aquatic training regimens (technical vs. game-based) on gross motor skills, stereotypy behavior and emotion regulation in children with ASD. Twenty-two autistic children were randomly assigned into three groups: two experimental groups performed either a technical aquatic program or a game-based aquatic program and a control group. Participants were assessed before and after an 8-week training period, with the Test of Gross Motor Development, the stereotypy subscale of the Gilliam Autism Rating Scale, and the Emotion Regulation Checklist. A significant effect for time was found in gross motor skills and stereotypy behavior in both experimental groups. An improvement in gross motor skills was observed in both experimental groups compared to the control group. A small pre-post change effect in emotion functioning was found in all groups. No significant differences were observed between the experimental groups in all assessed variables. Our findings provide additional evidence suggesting the effectiveness of beneficial effects of aquatic activities on the motor and social skills that underpin the hypothesis that motor and intellectual domains are highly interrelated in autistic children.