Lithium has been used as a mood-stabilizing drug in people with mood disorders. Previous studies have shown that natural levels of lithium in drinking water may protect against suicide. This study evaluated the association between lithium levels in tap water and the suicide standardized mortality ratio (SMR) in 40 municipalities of Aomori prefecture, which has the highest levels of suicide mortality rate in Japan. Lithium levels in the tap water supplies of each municipality were measured using inductively coupled plasma-mass spectrometry. After adjusting for confounders, a statistical trend toward significance was found for the relationship between lithium levels and the average SMR among females. These findings indicate that natural levels of lithium in drinking water might have a protective effect on the risk of suicide among females. Future research is warranted to confirm this association.