<p>Aquaporin 5 (AQP5) is crucial for salivary secretion, composition and enamel mineralization. Genetic variations in AQP5 may influence susceptibility to dental diseases such as caries. This study investigated the association between AQP5 single nucleotide polymorphisms (SNPs), AQP5 mRNA expression, and caries severity in a dental practice cohort. A total of 246 patients were enrolled. Caries experience was assessed using the decayed, missing, and filled (DMF) index, and salivary AQP5 mRNA expression was quantified by RT-qPCR. Genotyping included rs2878771, rs296763, rs3736309, and rs3759129. Statistical analyses comprised Chi-square testing, ROC analysis with Youden Index determination, and binary logistic regression adjusted for age and sex. The A allele of rs3736309 was associated with an increased risk of severe caries, particularly in patients over 60 years of age. AQP5 mRNA expression was higher in individuals with severe caries and in carriers of the C allele of rs2878771. ROC analysis identified an AQP5 expression cut-off (0.11274) that discriminated between severe and non-severe caries (AUC = 0.578, <i>p</i> = 0.048). Logistic regression confirmed AQP5 expression as an independent predictor of severe caries (<i>p</i> = 0.005). AQP5 expression and genetic variation appear to contribute to caries susceptibility in an age-dependent manner with moderate effects. The intronic variant rs3736309 was associated with caries severity. The biological mechanisms underlying this association remain unclear and require functional investigation. These findings support a potential role of AQP5 as an exploratory biomarker candidate for caries risk, particularly in elderly individuals.</p><p><i>Trial registration</i>: German Clinical Trial Registry No. DRKS00032425, date of registration: 2023-08-16.</p>