The water Cherenkov detector detects the Cherenkov radiation usually by photomultiplier tubes (PMTs), and the cone of emission can be reconstructed. The axis of the cone gives the direction of the particle, and the light yield gives the particle energy. Only charged particles with β > 1/n can be detected: this gives a threshold total energy of about 0.8 MeV for electrons, 160 MeV for muons and 1.4 GeV for protons and neutrons (somewhat higher in practice since the amount of Cherenkov radiation emitted exactly at threshold is negligible).
Neutrinos are detected in water Cherenkov when they interact by W exchange, converting into the equivalent charged lepton (muon or electron for νμ or νe respectively), or when they elastically scatter off electrons (when the recoil electron can be detected). Identifying ντ is more difficult, because of the short lifetime of the tau, but has been achieved by Super-K using the fact that tau decays often yield fast pions in the detector (Source: Sheffield.ac.uk).