Two common Potamogeton species, Potamogeton pectinatus L. and Potamogeton crispus L., were collected in 2016 and 2017 from a lowland, sandy bed in the Wilga River in Poland to investigate the ability of the plants to adapt to changing hydrological conditions. Measurements included biomechanical properties as well as the morphological characteristics of their stems. Specifically, experiments included three-point bending and tension tests as well as stem diameter and cross-sectional morphology at various periods in the plants’ life cycles. Detailed information about the seasonal changes in biomechanical traits and the similarities between the two investigated plants are presented. The data show significant differences in the three-point bending and tension parameters. The flexural rigidity proved to be the most sensitive parameter to changes in hydrological conditions during the season. The maximum forces in the three-point bending tests needed to complete the fracture of P. crispus were much higher, reaching values up to 0.097 N, than those for P. pectinatus (0.035 N), due to P. crispus having thicker shoots, which resulted in greater resistance to elastic deformity. Moreover, the modulus of elasticity values shows that P. pectinatus is much more prone to return to its original shape after the removal of the acting forces. For instance, the maximum Young’s modulus for P. pectinatus was 116.23 MPa, whereas for P. crispus, the highest value was four times lower (26.60 MPa). The present study supplements an aquatic plant biomechanics database that has been created in recent years.