Background: Dysphagia is common among stroke and acquired brain injury (ABI) patients and may result in aspiration. To reduce the risk of thin liquid aspiration, patients are often restricted to thickened fluids. There is considerable clinical interest in the risks and benefits of offering oral water intake, in the form of water protocols, to patients with thin-liquid dysphagia. Objectives: A controlled pilot study of a free water protocol was undertaken at Riverview Health Centre, in Winnipeg, Manitoba to assess benefits, feasibility and possible complications of free water protocol. Methods: The study examined 16 individuals with stroke or ABI who were randomly assigned to either a control group on thickened fluids (six subjects) or a treatment group (ten subjects) that followed a free water protocol. The average length of time in the study was 4.3 weeks with a range of 1-17 weeks among all participants. Results: Throughout the study, there was no incidence of pneumonia in any of the sixteen participants. No statistically significant difference was noted in the weekly total liquid intake between the treatment group and the control group. Perceived swallowing related care results suggest statistically significant improvements from initial to final measures for both the treatment group (p = 0.004) and the control group (p = 0.02). However, a comparison of the change in both measures, between the treatment and control groups, shows no statistically significant differences. Conclusion: This pilot study suggests the need for larger scale work in order to more accurately identify the effects of free water protocols.