When muons travel through matter, their energy losses lead to nuclear breakup (spallation) processes. The delayed decays of unstable daughter nuclei produced by cosmic-ray muons are important backgrounds for low-energy astrophysical neutrino experiments, e.g., those seeking to detect solar neutrino or Diffuse Supernova Neutrino Background (DSNB) signals. Even though Super-Kamiokande has strong general cuts to reduce these spallation-induced backgrounds, the remaining rate before additional cuts for specific signals is much larger than the signal rates for kinetic energies of about 6 -- 18 MeV. Surprisingly, there is no published calculation of the production and properties of these backgrounds in water, though there are such studies for scintillator. Using the simulation code FLUKA and theoretical insights, we detail how muons lose energy in water, produce secondary particles, how and where these secondaries produce isotopes, and the properties of the backgrounds from their decays. We reproduce Super-Kamiokande measurements of the total background to within a factor of 2, which is good given that the isotope yields vary by orders of magnitude and that some details of the experiment are unknown to us at this level. Our results break aggregate data into component isotopes, reveal their separate production mechanisms, and preserve correlations between them. We outline how to implement more effective background rejection techniques using this information. Reducing backgrounds in solar and DSNB studies by even a factor of a few could help lead to important new discoveries.
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