Bipolar electrochemistry has attracted great interest for applications based on sensing, electrografting, and electrodeposition, because the technique enables electrochemical reactions to be induced at multiple bipolar electrodes (BPEs) with only a single power supply. However, there are only a few reports on the biofabrication of hydrogels using BPEs. In this study, we applied bipolar electrochemistry to achieve the electrodeposition of calcium-alginate hydrogels at specified target areas, which is possible because of the use of water electrolysis to obtain acidification at the anodic pole. This scheme was used to successfully fabricate an array of hydrogel deposits at a BPE array. In addition, hydrogels were successfully fabricated either at only the target BPEs or only the target areas of BPEs by repositioning the driving electrodes. Furthermore, a hydrogel was drawn on a large BPE as a canvas by using small driving electrodes. As a demonstration of the electrodeposited hydrogels for bioapplications, mammal cells were cultured in the hydrogels. Because the amount and shape of the hydrogel deposits can be controlled by using the bipolar system, the system we developed can be used for biosensors and cell culture platforms.