Aquaporin-4 (AQP4) is a water channel found at high concentrations around blood vessels in the brain and is organized into elaborate assemblies called square arrays. The natural functions of AQP4 and the square arrays remain unknown, but under pathophysiological conditions, AQP4 has been shown to influence brain edema, synapse function, and cellular migration. AQP4 was recently found to have six isoforms, where AQP4a (also known as M1), AQP4c (also known as M23), and AQP4e are functional water transport channels. Furthermore, by two-dimensional blue native polyacrylamide gel electrophoresis (BN-PAGE) analysis of the internal composition of square arrays, three distinct isoforms were visualized. Here we combine these advances in technique with mutational analysis to test a series of current hypotheses about AQP4 functional structure. We find that the square array destabilizing N-terminus of AQP4a is partly functional through the C13 and C17 amino acids, and not through R8 and R9. We find a discrepancy between our data and the proposed tetramer-tetramer binding site based on the in vitro AQP4 two-dimensional crystal structure. On the other hand, we find that isoforms AQP4a and AQP4e, while not being able to form square arrays alone, are able to interact with AQP4c and be incorporated into higher-order structures. Our results with the novel BN-PAGE analysis technique point toward a model in which the presence of accessory isoforms (AQP4a and AQP4e) regulates the square array assembly process of the main isoform, AQP4c.