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Sustained and effective use of evidence-based practices in substance abuse treatment services faces both clinical and contextual challenges. Implementation approaches are reviewed that rely on variations of plan-do-study-act (PDSA) cycles, but most emphasize conceptual identification of core components for system change strategies. A two-phase procedural approach is therefore presented based on the integration of Texas Christian University (TCU) models and related resources for improving treatment process and program change. Phase 1 focuses on the dynamics of clinical services, including stages of client recovery (cross-linked with targeted assessments and interventions), as the foundations for identifying and planning appropriate innovations to improve efficiency and effectiveness. Phase 2 shifts to the operational and organizational dynamics involved in implementing and sustaining innovations (including the stages of training, adoption, implementation, and practice). A comprehensive system of TCU assessments and interventions for client and program-level needs and functioning are summarized as well, with descriptions and guidelines for applications in practical settings.