Polyhydroxyalkanoates (PHAs), a family of naturally occurring biodegradable polyester, are considered environmentally friendly alternatives to conventional commodity plastics derived from petrochemicals.; however, their molecular interaction in water has not been elucidated. Here, we investigated the surface- and contact time-dependent underwater interaction characteristics of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-co-4HB)), the most common PHA, using a surface forces apparatus (SFA). We found that PHA showed weak adhesion with functionalized surface and cohesion for a short-contact time (<30 mins) in the water. The adhesion to the functionalized surface was strong in the order of mica (negatively charged hydrophilic), APTES (positively charged hydrophilic), and PS (hydrophobic). However, the adhesive strength of PHA to the functionalized surfaces increased as contact time increased, which may be attributed to chain rearrangement, reorientation, or van der Waals forces of PHA in water. We also confirmed results similar to those for SFA by bulk testing on hydrophilic surfaces. As PHAs have attracted people’s attention as eco-friendly and biocompatible polymers, these results provide insights for the development of PHA-based composite, as well as for the biodegradation and fate of PHA post-use.