Spallation-induced radioactive isotopes can be produced when cosmic ray muons pass through the matter. The decay $\beta^{\pm}$ products (sometimes with $\gamma$ emission) from these radioactive isotopes are one of the major background for the study of solar, reactor and supernova relic neutrinos. Unlike scintillator experiment, such isotope production has not been exclusively measured in water experiment. We present here the first measurement of the production yields of radioactive isotopes induced by cosmic ray muon spallation in water using the low energy trigger data by fixing their lifetimes. Furthermore, the $^9$Li rate (yield) is better measured to be $(0.86\pm0.12\pm0.16)$ /kton/day or $(0.51\pm0.07\pm0.09) \times 10^{-7}\mu^{-1}g^{-1}cm^2$ by tagging the delayed neutrons. The measurement demonstrates for the first time that the $^9$Li would have a negligible effect on SuperK-Gd project for the search of supernova relic neutrinos. Agreement between data and theoretical calculations is generally better in water than in scintillator, except the case of spallation products $^8$Li/$^8$B and $^9$Li, which eject many nucleons from $^{16}$O.