Microplastics are a diffuse contaminant with various global sources, pathways, and sinks. This study aimed to backtrack microplastics across environments using metaproteomic and eDNA metabarcoding information stored within the ecocorona. Pristine polyamide (PA) fibers, polyethylene terephthalate (PET) fibers and fragments, and PET and PA preincubated in bovine serum albumin (BSA) were deployed into a tank housing Penaeus monodon to develop an ecocorona. Upon collection, BSA was detected within the ecocorona, along with P. monodon proteins, using mass spectrometry. BSA preincubation influenced the diversity and abundance of ecocorona proteins with pristine microplastics having more significantly enriched proteins. Most ecocorona proteins reflected the marine environment, confirming that the protein assemblage on microplastics records environmental signatures. Microplastic tracking was validated using polyethylene plastics unintentionally discharged from an aquaculture facility into Moreton Bay and collected after 7 days. Orthogonal Partial Least Square models predicted the source with 69–92% accuracy based on 16S eDNA taxa and 69–123% accuracy based on untargeted metaproteomics. Several identified taxa from both analyses were specific to the aquaculture source, including genera Leucothrix and Rugeria and species Salmo salar and P. monodon. Overall tracking of microplastics using the ecocorona proved effective over short time scales and reliably reflected the surrounding biological milieu.