Currently, aquatic exercise is among the most common physical activity modalities for children with neuromuscular and neurodevelopmental disorders. However, the outcome measures that should be routinely used by therapists working in this specific health-care context have not been widely studied. The purpose of the study was to identify and compare the content of outcome measures used in aquatic physiotherapy for children, employing the International Classification of Functioning, Disability and Health (ICF) as a framework. A literature review was used to identify aquatic functioning outcome measures for children with neuromuscular and neurodevelopmental disorders. Content comparison of outcome measures identified was linked to the ICF following the linking guidelines, and content-related metrics were used to analyze them. Four outcome measures were identified (HAAR, Conatser, WOTA 1 and 2, and SWIM), which contained a total of 116 meaningful concepts and were linked to 35 ICF 2nd level categories. The greatest number of items assessed activity and participation categories. Large differences were found in reference to the density of content. For content diversity, the measures were all below 0.5. The identified outcome measurements showed homogeneity with respect to the theoretical foundation; however, some differences were found in terms of content analysis.