Abstract Background Alarming rates of unhealthy alcohol, non-prescription drug, and tobacco use highlight the preventable health risks of substance abuse and the urgent need to activate clinicians to recognize and treat risky use. Screening, brief intervention, and referral to treatment (SBIRT) is an efficacious and effective processes to identify, reduce and prevent risky use of substances. This paper describes a study protocol testing implementation of a toolkit to enhance use of SBIRT in acute care settings to recognize and address patient risky alcohol, drug, and tobacco use. Methods This study uses a phased cluster randomized mixed method design to test nurse-led implementation of an SBIRT toolkit on one medical-surgical unit at 14 acute care hospitals (critical access, community and academic health centers). Medical surgical units will be randomly assigned to implement the SBIRT toolkit (engagement and communication, assessment, planning, training, and evaluation tools) or a wait-list usual care control group that begins implementation 6 months later. Primary endpoints are documentation of SBIRT delivery in randomly selected electronic medical records at baseline, 6 months and 12 months after group 1 implementation (61 records per unit per time period, N = 2562). Two surveys will be administered to unit nurses: smoking cessation activities will be assessed at baseline and SBIRT use will be assessed on randomly-selected days after implementation. In addition, site coordinators will complete a baseline capacity assessment, an implementation fidelity survey post-implementation, and a structured interview at the end of the study. Multilevel mixed-effects effects logistic and linear models will be used to analyze use of SBIRT and cost outcomes. Discussion This study will guide subsequent SBIRT implementation, dissemination, and spread across rural, community and urban healthcare systems throughout the state and beyond. The long-term objective is to activate clinicians to recognize, intervene and refer people with risky substance use to improve health and decrease substance use disorders. Trial registration ClinicalTrials.gov NCT03560076