The incidence of chronic kidney disease (CKD) in children and adults is increasing. Cardiologists have become indispensable members of the care provider team for children with CKD. This is partly due to the high incidence of CKD in children and adults with congenital heart disease, with current estimates of 30–50%. In addition, the high incidence of acute kidney injury (AKI) due to cardiac dysfunction or following pediatric cardiac surgery that may progress to CKD is also well documented. It is now apparent that AKI and CKD are uniquely intertwined as interconnected syndromes. Furthermore, the well-known long-term cardiovascular morbidity and mortality associated with CKD require the joint attention of both nephrologists and cardiologists. Children with both congenital heart disease and CKD are increasingly surviving to adulthood, with synergistically negative medical, financial, and quality of life impact. An improved understanding of the epidemiology, mechanisms, early diagnosis, and preventive measures is of importance to cardiologists, nephrologists, scientists, economists, and policy makers alike. Herein, we report the current definitions, epidemiology, and complications of CKD in children, with an emphasis on children with congenital heart disease. We then focus on the clinical and experimental evidence for the progression of CKD after episodes of AKI commonly encountered in children with heart disease, and explore the role of novel biomarkers for the prediction of CKD progression.