Deep Eutectic Solvents (DESs) are emerging in the recent literature as promising environmentally friendly liquids in different topics, finding fruitful applications as substitutes to common volatile organic solvents. These mixtures are prepared via non-solvent procedures and they have peculiar structural features and properties. They are formed via weak interactions, mainly H-bonds, between two species; the interactions between the different species as well as the ones occurring between the same species, lead to an impossible regular crystal lattice formation, therefore leading to liquid systems. The number of novel DESs mixtures present in the literature is rapidly increasing because of the wide number of H-bonds capable molecules available. One of these classes is represented by aquoDESs: binary mixtures in which one of the components is water, confirmed in their DESs’ identity by theoretical/experimental melting curves approaches. In this work a study of cluster formation of water-based DESs in water dilutions is presented. The three analysed mixtures are: glycolic acid/water (GA/H2O); betaine/water (TMG/H2O), choline chloride/water (ChCl/H2O). Ionic conductivity, viscosity, ultrasound spectroscopy and NMR measures showed the presence of aggregates of aquoDESs in water dilutions until values about 50% w/w of added water. Finally, taking into account the convenient disposal as water dilution of a DES, the cytotoxicity of these dilutions was evaluated on Caco2 model cells, showing the effect to be related only to the non-water components of these liquids.