There are many causes of hydronephrosis. In adults, the conditions that most often cause hydronephrosis include: 1  Kidney stones —Salts and minerals that are present in urine can form small hard stones that may become lodged in the kidneys or urinary tract.ther possible causes of hydronephrosis include: 1  Blood clots in the kidney or ureter. 2  Narrowing or stricture of the urinary tract due to injury, infection, birth defects or surgery.