Water kefir is a plant-based type of kefir and has significant differences from well-known milk kefir. Recently, various complicated substrates were fermented with water kefir grains, but an economical substrate is essential for the industrial aspect. This study aims to understand changes in fermentation products of water kefir grains during fermentation with economic substrates and investigates how fermentation progresses under almost ideal fermentation parameters. The fig-based medium provided high contents of Lactobacillus spp. and Lactococcus spp. Also, fig-based medium with high fructose content contained a higher amount of Bifidobacterium sp. Moreover, the fig-based medium resulted in more organic acid content, forming as much as ten times higher than the sugar-based medium for lactic acid after the same fermentation time (p < 0.05). On the other hand, volatile compounds such as acetaldehyde, ethyl acetate, ethanol, acetic acid, 2-ethyl-1-hexanol, oxime-, methoxy-phenyl, and phenylethyl alcohol were detected for both water kefir samples. Antioxidant capacity (TEAC and ORAC) was higher for the fig-based medium than for the sugar-based medium. This is the first study that comprehensively proved that only sugar solution was not a sufficient medium for water kefir fermentation, but fig containing solution had abundant nutrients to obtain preferable and acceptable water kefir beverage.