Purpose: To evaluate the water equivalency of PRESAGE and genipin gel for 3D proton dosimetry. Methods: The GEANT4 Hadrontherapy example was modified to calculate depth doses in four different formulations of PRESAGE dosimeters and in water for a proton beam with a mean energy of 62 MeV. To compare the depth doses in each phantom, the water equivalent thickness (WET) was calculated for each PRESAGE dosimeter according to IAEA technical report 398. Results: Our GEANT4 results show that the maximum energy deposition occurs at 2.9 cm depth in water, at 2.7 cm in the two new chemical formulations of PRESAGE®, at 2.6 cm in the original formulation of PRESAGE®, at 2.55 cm in PRESAGETM and at 2.85 cm in genipin gel. The deposited energy in PRESAGETM is 15% higher than that in water, while it is approximately 5% higher than water in the new formulations of PRESAGE®. For the calculated relative dose versus WET, the new PRESAGE® dosimeters are in better agreement with the depth doses in water. At Bragg peak the maximum relative dose difference with that of water is up to 1% for the PRESAGE® formulation A and more than 2% for the PRESAGE® formulation B and C and the PRESAGETM dosimeter. For the genipin gel the maximum relative dose difference with water is less than 0.5%. Conclusions: The PRESAGE® dosimeters with the new chemical formulations are more water equivalent than the existing PRESAGE® and PRESAGETM dosimeters and are thus more suitable for accurate 3D dosimetry of proton beams. The depth dose in the genipin gel dosimeter shows better agreement with water than the PRESAGE dosimeters. Further experimental studies are planned to investigate possible saturation in the new PRESAGE® formulations and in genipin gel for high LET radiation fields.