Background: The free water protocol (FWP) is an alternate management strategy for patients with dysphagia, who would otherwise be nil by mouth or prescribed thickened fluids, allowing them to drink and potentially aspirate water under strict guidelines to minimize the risk of adverse consequences. The FWP is not widely implemented in acute settings, and it is unclear whether this is due to the complexity of patient presentations, clinician decision-making or barriers related to the setting. Aims: To explore the perceptions and decision-making process of clinicians about using FWPs to manage dysphagia for patients admitted to acute stroke and general medicine. Methods & Procedures: A qualitative, critical realist approach was adopted to allow for in-depth exploration of the perspectives of four dietitians, seven medical officers, eight registered nurses and 17 speech and language pathologists (SLPs) from three hospitals in a capital city of Australia. Data from semi-structured interviews were analysed using the Situated Clinical Decision-Making Framework (CDF). Outcomes & Results: Participants were cautious about FWP for patients with neurological conditions, head and neck cancer, dementia, poor immunity, chronic or recurrent respiratory illness, and certain types of stroke. Medical status and the implications for aspiration were paramount, particularly respiratory status, oxygen supplementation, cognitive status, fatigue and mobility. Participants considered patient quality of life, preferences and choices for care, but indicated that factors influencing safety often outweighed patient preference for water. Indirect factors affecting decision-making included the roles of the multidisciplinary team, individual clinical experience and attitude to risk, and availability of supervision. Conclusions & Implications: Despite the benefits of FWPs in other settings, in acute stroke and general medicine, clinicians erred on the side of safety and, in most cases, would not implement an FWP. Future clinical research is needed to systematically design high-quality and feasible clinical trials to determine the benefits and safety of FWPs for patients with dysphagia in these settings. This would lay the foundations for guidelines to support the complex clinical decision-making regarding patient suitability for FWPs.