Background Kidney disease is the most important predictor of death in patients with a Fontan circulation, yet its clinical and hemodynamic correlates have not been well established. Methods and Results A total of 53 ambulatory patients with a Fontan circulation (median age, 16.2 years, 52.8% male patients) underwent advanced cardiovascular magnetic resonance assessment, including 4‐dimensional flow imaging and computational fluid dynamics. Estimated glomerular filtration rate (eGFR) <90 mL/min per 1.73 m ² was observed in 20.8% and albumin‐to‐creatinine ratio >3 mg/mmol in 39.6%. The average eGFR decline rate was −1.83 mL/min per 1.73 m ² per year (95% CI, −2.67 to −0.99; P <0.001). Lower eGFR was associated with older age, larger body surface area at examination, longer time since Fontan procedure, and lower systemic ventricular ejection fraction. Higher albumin‐to‐creatinine ratio was associated with absence of fenestration at the Fontan operation, and older age and lower systemic ventricular ejection fraction at the assessment. Lower cross‐sectional area of the Fontan conduit indexed to flow (r=0.32, P =0.038), higher inferior vena cava–conduit velocity mismatch factor (r=−0.35, P =0.022), higher kinetic energy indexed to flow in the total cavopulmonary connection (r=−0.59, P =0.005), and higher total cavopulmonary connection resistance (r=−0.42, P =0.005 at rest; r=−0.43, P =0.004 during exercise) were all associated with lower eGFR but not with albuminuria. Conclusions Kidney dysfunction and albuminuria are common among clinically well adolescents and young adults with a Fontan circulation. Advanced cardiovascular magnetic resonance–derived metrics indicative of declining Fontan hemodynamics are associated with eGFR and might serve as targets to improve kidney health. Albuminuria might be driven by other factors that need further investigation.