Expression of AQP3 and associated EMT proteins predict poor prognosis of GC. Patients that overexpressed AQP3 demonstrated shorter OS than those in the low expression group (P = 0.038). Patients with lower expression levels of E-cadherin had a worse OS than those with high E-cadherin expression levels (P = 0.008). Patients that were positive for vimentin expression exhibited poor survival rates compared with those who were negative for vimentin (P = 0.048). Patients with high expression levels of AQP3 but lacked E-cadherin and vimentin had a worse OS (P = 0.028).