Executive functions (EF) are higher-order cognitive processes that support goal-directed behavior, learning, and adaptation. Children with autism spectrum disorder (ASD) and intellectual disability (ID) often show EF deficits that affect attention, planning and self-regulation. Although visual and physically engaging interventions can improve EF, their combined use in aquatic programs remains underexplored. This study investigated the effects of an adapted swimming program with visual prompts on EF and frontal lobe activation in children with ASD and ID. Twenty-nine children aged 6–15 years (19 with ASD, 10 with ID) were randomly assigned to an experimental group (EG; n = 17) or control group (CG; n = 12). The EG completed a 14-week adapted swimming program (two 60-minute sessions/week) with visual supports that include picture cards and short video prompts. Executive performance was assessed pre- and post-intervention using an exergame (‘Squid Hero for Kinect’ by Visual Air Guitar Company) that measured score and completion time, while dorsolateral prefrontal cortex activation was monitored via fNIRS (HbDiff). Post-intervention, the EG showed significantly higher exergame scores than the CG (p = .012), with improvements observed in both ASD and ID subgroups; ID participants in the EG outperformed their CG counterparts (p = .011). No group differences were found in completion time or overall HbDiff, though post-intervention HbDiff differed between ASD and ID within the EG, which indicated distinct neural engagement patterns. Overall, the findings indicate that an adapted swimming program enriched with visual prompts may support improvements in visual–motor processing and executive task performance in children with ASD and ID. Although neurophysiological changes in prefrontal activation were limited, the results highlight the potential of visually structured aquatic interventions as a complementary approach for enhancing cognitive and motor functioning in children with neurodevelopmental disorders.