Aquaporin 5 (AQP5) is a water channel protein that is over-expressed in many tumors. Elevated expression of AQP5 is associated with poor prognosis of colorectal cancer. Yet, whether AQP5 plays a role in epithelial-mesenchymal transition (EMT) of colorectal cancer has not been reported until now. Here we aim to investigate the function of AQP5 in the EMT process of colorectal cancer. We transfected HCT116 and SW480 cells with AQP5-specific shRNA and verified the knockdown efficiency through western blotting and real-time PCR. Afterwards, scratch wound healing assay, invasion assay, gelatin zymography, immunofluorescence staining and immunoblotting were performed to assess the effect of AQP5 silencing in these two cells. The ability of migration and invasion of colorectal cancer cells was significantly impaired after AQP5 silencing. Correspondingly, the activity and expression of Matrix Metallopeptidase (MMP)-2 and MMP-9 were reduced. Moreover, the expression levels of EMT-related factors were altered: E-cadherin, Tissue Inhibitor Of Metalloproteinases (TIMP)-1 and TIMP-2 were upregulated, whereas Vimentin, N-cadherin, Plasminogen Activator, Urokinase (uPA) and Snail were downregulated following knockdown of AQP5 in colorectal cancer cells. Furthermore, the expression of Wnt1 and β-catenin was markedly decreased after AQP5 knockdown. Interestingly, the alteration of EMT-related factors mediated by AQP5 knockdown could be reversed by upregulation of β-catenin. Taken together, silencing of AQP5 restrained the migration and invasion of colorectal cancer cells, and regulated the expression of EMT-related molecules in them by inhibiting Wnt/β-catenin pathway.