Saliva produced by the salivary glands is critical for oral health. The respiratory and digestive systems could be negatively affected by trauma to these glands. This study investigates the impact of three water types on salivary gland function at molecular and histopathological levels using twenty-one male albino rats divided into three groups. The control group (Group I) consumed regular tap water, while Group II was given magnetic water, created by passing water through a 14500 Gauss magnetic field. Group III received microwave-heated tap water. Following a 60-day period and overnight fasting, rats were euthanized for salivary gland analysis. Results indicated significant body and salivary gland weight reductions, particularly in the microwave water group, which also showed decreased mRNA expression for MUC7, MUC19, HTN1, HTN3, CST2, and CST4 genes and increased amylase and HDAC3 expression. In contrast, magnetic water rats exhibited increased mRNA expression for MUC7, MUC19, CST2, and CST4 compared to the tap water group. Histopathological analysis revealed abnormal acini architecture and vacuolization in microwave-treated rats, along with significantly stronger BCL-2 expression in the tap and magnetic water groups than in the microwave water group, highlighting microwave-treated water's detrimental effects on salivary glands.