Chronic Kidney Disease (CKD) is a progressive disorder characterized by irreversible structural and functional alterations of the kidneys, ultimately leading to a decline in glomerular filtration rate and systemic complications. The kidney’s complex architecture, comprising glomeruli, renal tubules, interstitium, and vasculature, undergoes sequential pathological changes during the course of CKD. Early functional disturbances are often subtle, whereas advanced stages are marked by overt anatomical derangements such as glomerulosclerosis, tubular atrophy, interstitial fibrosis, and vascular sclerosis. Understanding the applied anatomy of the kidney and its structural remodeling is essential for correlating clinical manifestations, laboratory abnormalities, and radiological findings. This review analyzes the applied anatomy of the kidney with emphasis on structures affected in CKD and examines microscopic, macroscopic, and radiological structural changes using evidence from anatomical descriptions, histopathology, imaging studies, and contemporary nephrology literature. Structural alterations involving the glomerulus, renal tubules, interstitium, and renal vasculature are correlated with functional consequences including proteinuria, impaired urine concentrating ability, electrolyte imbalance, anemia, and progressive decline in renal function. Radiological features such as reduced renal size, cortical thinning, increased cortical echogenicity, and loss of corticomedullary differentiation reflect irreversible nephron loss and chronic scarring. The applied anatomical changes observed in CKD form the structural basis for its diverse clinical, biochemical, and radiological manifestations, and an integrated understanding of renal anatomy, histology, and imaging provides a comprehensive framework for early diagnosis, prognostication, and effective management of Chronic Kidney Disease.