We sought to qualitatively evaluate impediments in implementing a novel Screening, Brief Intervention and Referral to Treatment (SBIRT) protocol into normal emergency department (ED) workflow for patients with at-risk drug/alcohol behavior. From 2010, administrative and nursing champions trained nurses at a single ED (census: 50,000 visits/yr) in SBIRT and incorporated SBIRT into normal ED nursing workflow in 2012. To qualitatively analyze impediments in SBIRT implementation, we created a semi-structured questionnaire for protocol champions with subsequent follow-up. Investigators analyzed responses using qualitative methodology based on a modified grounded theory framework. In 2012, 47693 visits by 31525 patients met SBIRT protocol initiation criteria with a protocol execution rate of 83.4%. Interview data identified the following impediments: (1) Need for multi-layer leadership support; (2) Application of an overarching vision to constantly address personnel attitudes towards SBIRT appropriateness in the ED; (3) Continuous performance monitoring to address implementation barriers close to real time; (4) Strategic and adaptive SBIRT training; and (5) External systemic changes through internal leadership. Qualitative analysis suggests that impediments to SBIRT implementation in the ED include views of SBIRT appropriateness in the ED, need for continuous reinforcement/refinement of personnel training / protocol execution, and fostering of additional administrative/financial champions