The aim of this work is to analyze the effect of water absorption on the mechanical properties and damage mechanisms of polyester/glass fiber/jute fiber hybrid composites obtained using the compression molding and vacuum-assisted resin transfer molding (VARTM) techniques with different stacking sequences. For this purpose, the mechanical behavior under tensile stress of the samples was evaluated before and after hygrothermal aging at different temperatures: TA, 50 °C, and 70 °C for a period of 696 h. The damage mechanism after the mechanical tests was evaluated using SEM analysis. The results showed a tendency for the mechanical properties of the composites to decrease with exposure to an aqueous ambient, regardless of the molding technique used to conform the composites. It was also observed that the stacking sequence had no significant influence on the dry composites. However, exposure to the aqueous ambient led to a reduction in mechanical properties, both for the molding technique and the stacking sequence. Damage such as delamination, fiber pull-out, fiber/matrix detachment, voids, and matrix removal were observed in the composites in the SEM analyses.