Water-assisted ultrashort laser pulse processing of semiconductor materials is a promising technique to diminish heat accumulation and improve process quality. In this study, we investigate femtosecond laser ablation of deep trenches in GaAs, an important optoelectronic material, using water and ambient air environments at different laser processing regimes. We perform a comprehensive analysis of ablated trenches, including surface morphological analysis, atomic-resolution transmission electron microscopy imaging, elemental mapping, photoluminescence, and Raman spectroscopy. The findings demonstrate that GaAs ablation efficiency is enhanced in a water environment while heat-accumulation-related damage is reduced. Raman spectroscopy reveals a decrease in the broad feature associated with amorphous GaAs surface layers during water-assisted laser processing, suggesting that a higher material quality in deep trenches can be achieved using a water environment.