Self-management in chronic kidney disease (CKD) can slow disease progression; however, there are few tools available to support patients with early CKD. My Kidneys My Health is a patient-focused electronic health (eHealth) self-management tool developed by patients and caregivers. This study will investigate the implementation of My Kidneys My Health across primary care and general nephrology clinics. The study aims to: (1) identify and address barriers and facilitators that may impact implementation and sustainability of the website into routine clinical care; (2) evaluate implementation quality to inform spread and scale-up. We will conduct a multi-stage approach using qualitative methods, guided by the Quality Implementation Framework and using a qualitative content analysis approach. First, we will identify perceived barriers and facilitators to implementation and considerations for sustainability through interviews with clinicians, based on the Readiness Thinking Tool and the Long Term Success Tool. Analysis will be guided by the Consolidated Framework for Implementation Research and the Theoretical Domains Framework. Appropriate implementation strategies will be identified using the Expert Recommendations for Implementing Change compilation, and implementation plans will be developed based on Proctor’s recommendations and the Action, Actor, Context, Target, Time framework. Finally, we will explore implementation quality guided by the RE-AIM framework. There is limited literature describing systematic approaches to implementing and sustaining patient-focused self-management tools into clinical care, in addition to employing tailored implementation strategies to promote adoption and sustainability. We aim to generate insights on how My Kidneys My Health can be integrated into clinical care and how to sustain use of patient-centric eHealth tools in clinical settings on a larger scale.