It is highly challenging to detect the pathophysiology of the diseased kidneys and achieve precise diagnosis because there are few in vivo noninvasive imaging techniques to quantitatively assess kidney dysfunction. This longstanding challenge is normally attributed to the limited molecular contrast agents which can be addressed with renal clearable nanoprobes. In this report, we demonstrate the use of magnetic resonance imaging along with renal clearable ferric coordination polymer nanodots (Fe-CPNDs) for in vivo monitoring the kidney dysfunction effects following drug (daunomycin)-induced kidney injury. After intravenous injection of Fe-CPNDs, the change of the MR signal in the kidney can be precisely correlated with local pathological lesion which is demonstrated by renal anatomic details and biochemical examinations of urine and blood. This finding opens the door to the possibility of noninvasively assessing kidney dysfunction and local injuries.