Although the number of reports demonstrating the roles of individual aquaporins in plants under diverse physiological conditions is expanding, the importance of interactions between different aquaporin isoforms and their integrated functions under stress conditions remain unclear. Here, we expressed one cucumber aquaporin gene, designated CsPIP1;1, and one figleaf gourd aquaporin gene, designated CfPIP2;1, in Arabidopsis thaliana, and investigated the effect of its expression on the natural expression patterns of endogenous PIP genes under stress conditions. The transcript levels of endogenous Arabidopsis PIP members were altered differently depending on stress conditions by the expression of CsPIP1;1 or CfPIP2;1. The transgenic Arabidopsis plants that constitutively express CfPIP2;1 displayed better growth compared with the wild-type plants under dehydration stress conditions, whereas CsPIP1;1 expression exerted a negative effect on the growth of Arabidopsis under dehydration stress conditions. CsPIP1;1 or CfPIP2;1 expression facilitated seed germination under high salt stress conditions, but had no influence on the growth of Arabidopsis under cold stress conditions. Our results indicate that the ectopic expression of a foreign aquaporin gene perturbs differently the natural expression patterns of endogenous aquaporin genes depending on particular stress conditions, and thereby influences the responses of plants to different stress conditions. This implies that the up- and/or down-regulation of aquaporins and their integrated functions are crucial to the maintenance of proper water balance under stress conditions.