Abstract Background Excessive sugar consumption remains implicated as one of the key dietary factors that has been linked to overweight and obesity in children. Schools have been identified as an important setting for health promotion interventions in children and can be successful in bringing about dietary behavioral change when well designed. Objective The main aim of the study was to conduct a pilot intervention study and assess the possible effects of educational and environmental methodological components on sugar intake and water consumption in Maltese school children. Subjects and methods Face-to-face educational sessions for children and parents were supported by written materials and provision of free drinking water for children for a 12 week period in the school setting. Two main dietary outcomes were measured: non-milk extrinsic sugars(NMES) intake (measured as g/day) and water consumption (measured as servings/day), measured in the pre- and post-intervention periods. The dietary outcomes were measured at school using the novel online dietary assessment tool, REALITYMALTA™. Results 55 children, aged 10-11 years, were recruited, and 48 provided diet data at baseline and end. A reduction in mean energy intakes was noted from 7733 kJ/day (SD 2046) to 6809 (SD 2224) kJ/day (p = 0.03), with water servings intake increased and NMES intake decreased but results not statistically significant. Parent attendance at the educational sessions was low. Conclusions A larger scale study, including multi-level analysis is recommended. Modifying the content of the intervention and finding ways to increase parent engagement should be considered in future.