Substances like calcium, phosphorus, oxalate and uric acid are normally excreted in the urine. 

These substances are kept in a dissolved state due to the presence of certain chemicals in the urine known as “stone inhibitors”. Some stone forming substances are kept soluble due to a specific pH of the urine. 

These substances start crystallizing and forming stones in situations like Stagnation of urine due to obstruction in the urinary tract or inadequate evacuation of urinary bladder. 

Infections of the kidney with certain bacteria lead to triple phosphate stone formation. In some patients deficiency of stone inhibitors lead to repeated stone formation. Changes in urinary pH also enhance crystallization, just as uric acid crystals gather to form stones in an acidic urine. 

Super saturation of urine with stone forming substances can occur if Concentrated urine due to a decreased intake of water specially in hot climates Increased excretion of calcium, oxalate and uric acid in the urine. Calcium in the urine may be increased in situations like. 

Some familial disease where either there is an increased absorption from the intestine or increased excretion of calcium from the kidney. Increased intake of Vitamin D which increases calcium level in the blood. Excessive intake of calcium containing diet such as milk and use of certain drugs like antacids for dyspepsia (heart burn). 

Certain diuretics increase the urinary calcium excretion. Increased activity of a gland situated in the neck called the Parathyroid gland. The increased activity of parathyroid glands causes increased calcium level in the blood and increased excretion in the urine. 

Oxalate may be increased in the urine due to Increased intake of oxalate containing diet such spinach, nuts, chocolate and tea. Increased absorption due to some gut disease or resection of the last part of the small intestine called the ileum. 

Deficiency of a specific type of enzyme in the liver needed for the destruction of oxalate present in the body. Vitamin C is metabolized into oxalate, so increased intake may cause oxalate stone. Uric acid stones can precipitate when its blood levels are increased. Increased uric acid levels can result in deposition of the crystals causing Gout. 
However in some conditions urine may become saturated without its high blood levels. 

Note: Most of the time kidney stones are formed without any apparent cause.