Magnesium citrate has some scientific support for use in the prevention of kidney stones, particularly calcium oxalate stones, which are the most common type. Several studies have shown that magnesium can inhibit the formation of these stones by binding to oxalate in the gut, forming insoluble magnesium oxalate that is excreted in the feces rather than absorbed and later excreted by the kidneys. This reduces urinary oxalate levels, a key risk factor for stone formation. Magnesium may also reduce the supersaturation of calcium oxalate in urine, further decreasing stone risk.

Clinical studies and meta-analyses have found that supplementation with magnesium, often combined with citrate (which itself can also inhibit stone formation), can reduce the recurrence rate of kidney stones in some patients. Magnesium citrate is sometimes preferred because both magnesium and citrate have stone-inhibiting properties: citrate binds to urinary calcium, reducing the likelihood of stone formation.

However, the overall quality of evidence is moderate (hence the rating of 3). Not all studies have found a benefit, and most guidelines suggest magnesium supplementation only in select patients, such as those with confirmed low urinary magnesium or recurrent stone formers. Magnesium citrate is not typically used as a first-line therapy but is a reasonable adjunct in certain cases.