Difficult-to-remove microplastic pollution poses serious risks to ecosystems and human health. Sewage treatment plants also cannot remove microplastics completely with filters or harsh chemical treatments. It is imperative to develop biotechnologies that aggregate microplastics into larger sizes for rapid removal from polluted waters. Using experimental evolution, we generated microplastic aggregators (MAGs) from the environmentally prevalent Pseudomonas aeruginosa, which are evolved to aggregate microplastics into sizable aggregates via biofilm formation. This is mediated by upregulation of a cyclic-di-GMP (c-di-GMP) secondary messenger signaling system found in most bacterial species. Comparative genomic analysis of MAGs revealed mutations in the yfiR gene, which is the repressor of tpbB, a c-di-GMP synthesizing diguanylate cyclase (DGC). Derepression of tpbB conferred MAGs with high intracellular c-di-GMP content and production of a CdrA biofilm matrix protein, resulting in higher biofilm formation and aggregation of microplastics with various sizes and materials. To release microplastics from the aggregates for downstream resource recovery, we employed protease (trypsin) to degrade CdrA and disrupt the biofilm matrix. As a proof-of-concept method, we demonstrated that a capture-then-release approach could mitigate microplastic pollution in seawater samples collected in the vicinity of a sewage outfall. Hence, our work provides insights into efficient biological removal of other micropollutants or biofilm-enabled catalysis of microparticles.