This dataset contains bottom-up LC-MS/MS data from culture-supernatant-derived extracellular protein fractions of natural seawater microbial communities incubated under three conditions: a polymer-free control (Marine Blank), amorphous polyhydroxyalkanoate (aPHA), and semi-crystalline polyhydroxyalkanoate (scPHA). The aPHA and scPHA substrates contained the same constituent monomers but differed in their monomer composition ratios and physical states. Raw mass spectra were searched against a protein sequence database derived from an Alcanivorax genome. The resulting protein identifications therefore represent proteins matching the Alcanivorax genome-derived proteome within a mixed marine microbial community. This dataset is intended as a descriptive, genome-informed extracellular metaproteomic resource and should not be interpreted as definitive organism-specific protein assignments.