We investigated whether aquaporin-4 (AQP4) single-nucleotide polymorphisms (SNPs) influence Alzheimer's disease (AD) progression through changes in the glymphatic system. We included 242 non-dementia participants and chose six SNPs previously shown to be related to AD. We analyzed the associations between AQP4 SNPs and glymphatic markers, including enlarged perivascular spaces (PVS), white matter free water (FW), and diffusion tensor image analysis along the perivascular space (DTI-ALPS), in both cross-sectional and longitudinal data. We investigated whether AQP4-related glymphatic markers are associated with AD pathology progression and cognitive impairment, and whether they mediate the relationship between AQP4 SNPs and AD progression. There was no association between AQP4 SNPs and glymphatic markers at baseline. Carriers of the AQP4 SNP rs72878794 minor allele status exhibited slower FW increase in the amyloid-positive group (SNP*time: β = -0.0040, t(46.25) = -2.062, p = 0.045, 95% CI = -0.0078 ~ -0.0002), whereas the rs9951307 minor allele carrier showed a faster FW increase in the amyloid-negative group (SNP*time: β =0.0033, t(81.19) = 2.245, p = 0.027, 95% CI = 0.0004 ~ 0.0062). The higher FW was associated with faster cognitive decline at follow-ups. AQP4 SNPs influence interstitial fluid accumulation, contributing to cognitive decline but not amyloid deposition in AD. Further studies are needed to clarify the pathways linking AQP4 SNPs and AD progression.