The benefit of water protocols for individuals with thin liquid aspiration remains controversial, with mixed findings from a small number of randomized controlled trials (RCTs). This study aimed to contribute to the evidence of the effectiveness of water protocols with a particular emphasis on health outcomes, especially hydration. An RCT was conducted with patients with known thin liquid aspiration post stroke randomized to receiving thickened liquids only or a water protocol. For the 14 participants in rehabilitation facilities whose data proceeded to analysis, there was no difference in the total amount of beverages consumed between the water protocol group (mean = 1103 ml per day, SD = 215 ml) and the thickened liquids only group (mean = 1103 ml, SD = 247 ml). Participants in the water protocol group drank on average 299 ml (SD 274) of water but offset this by drinking less of the thickened liquids. Their hydration improved over time compared with participants in the thickened liquids only group, but differences between groups were not significant. Twenty-one percent of the total sample was diagnosed with dehydration, and no participants in either group were diagnosed with pneumonia. There were significantly more diagnoses of urinary tract infection in the thickened liquids only group compared to the water protocol group (χ2 = 5.091, p = 0.024), but no differences between groups with regard to diagnoses of dehydration (χ2 = 0.884, p = 0.347) or constipation (χ2 = 0.117, p = 0.733). The findings reinforce evidence about the relative safety of water protocols for patients in rehabilitation post stroke and provide impetus for future research into the potential benefits for hydration status and minimizing adverse health outcomes.