High-repetition-rate low-pulse-energy near-infrared femtosecond laser pulses from a Ti:sapphire oscillator were used to micromachine localized refractive index structures inside ophthalmologic hydrogel polymers. The relation between laser-induced refractive index modification and different laser micromachining conditions was investigated in both pure and dye copolymerized hydrogel polymers. We studied the nonlinear absorption enhancement of the laser energy induced by copolymerized dyes during the micromachining process and the effects on increasing the laser scanning speed. We discussed the wavelength dependence and the laser pulse energy dependence of the micromachining results in a laser operation wavelength range from $700\mathrm{nm}\text{to}1000\mathrm{nm}$ . By changing the water concentration in pure and doped hydrogel polymers, we further investigated the critical role that water plays in the creation of large refractive index modifications in hydrogels without inducing optical breakdown or damage. A thermal model was used to explain the experimental results. By increasing nonlinear absorption in hydrogel polymers and optimizing femtosecond laser operation parameters, large refractive index modifications could be achieved with greatly increased laser micromachining speeds. In this paper, we discuss the optimization of material and laser parameters for the hydrogel material system.