Following from our previous Letter on this topic, this Article reports a detailed study of time-of-flight-secondary ion mass spectrometry (TOF-SIMS) positive ion spectra generated from a set of model biocompounds (arginine, trehalose, DPPC, and angiotensin II) by water cluster primary ion beams in comparison to argon cluster beams over a range of cluster sizes and energies. Sputter yield studies using argon and water beams on arginine and Irganox 1010 have confirmed that the sputter yields using water cluster beams lie on the same universal sputtering curve derived by Seah for argon cluster beams. Thus, increased ion yield using water cluster beams must arise from increased ionization. The spectra and positive ion signals observed using cluster beams in the size range from 1 000 to 10 000 and the energy range 5–20 keV are reported. It is confirmed that water cluster beams enhance proton related ionization over against argon beams to a significant degree such that enhanced detection sensitivities from 1 μm2 in the region of 100 to 1 000 times relative to static SIMS analysis with Ar2000 cluster beams appear to be accessible. These new studies show that there is an unexpected complexity in the ionization enhancement phenomenon. Whereas optimum ion yields under argon cluster bombardment occur in the region of E/n ≥ 10 eV (where E is the beam energy and n the number of argon atoms in the cluster) and fall rapidly when E/n <10 eV; for water cluster beams, ion yields increase significantly in this E/n regime (where n is the number of water molecules in the cluster) and peak for 20 keV beams at a cluster size of 7 000 or E/n ∼3 eV. This important result is explored further using D2O cluster beams that confirm that in this low E/n regime protonation does originate to a large extent from the water molecules. The results, encouraging in themselves, suggest that for both argon and water cluster beams, higher energy beams, e.g., 40 and 80 keV, would enable larger cluster sizes to be exploited with significant benefit for ion yield and hence analytical capability.