Welding technology may be considered as a promising processing method for the formation of packaging products from biopolymers. However, the welding processes used can change the properties of the polymer materials, especially in the region of the weld. In this contribution, the impact of the welding process on the structure and properties of biopolymer welds and their ability to undergo hydrolytic degradation will be discussed. Samples for the study were made from polylactide (PLA) and poly(3-hydroxyalkanoate) (PHA) biopolymers which were welded using two methods: ultrasonic and heated tool welding. Differential scanning calorimetry (DSC) analysis showed slight changes in the thermal properties of the samples resulting from the processing and welding method used. The results of hydrolytic degradation indicated that welds of selected biopolymers started to degrade faster than unwelded parts of the samples. The structure of degradation products at the molecular level was confirmed using mass spectrometry. It was found that hydrolysis of the PLA and PHA welds occurs via the random ester bond cleavage and leads to the formation of PLA and PHA oligomers terminated by hydroxyl and carboxyl end groups, similarly to as previously observed for unwelded PLA and PHA-based materials.