Silver nanoparticles (AgNPs) demonstrating good antimicrobial activity are widely used in many fields. However, the impact of AgNPs on the community structures of marine biofilms that drive biogeochemical cycling processes and the recruitment of marine invertebrate larvae remains unknown. Here, we employed MiSeq sequencing technology to evaluate the bacterial communities of 28-day-old marine biofilms formed on glass, polydimethylsiloxane (PDMS), and PDMS filled with AgNPs and subsequently tested the influence of these marine biofilms on plantigrade settlement by the mussel Mytilus coruscus. AgNP-filled PDMS significantly reduced the dry weight and bacterial density of biofilms compared with the glass and PDMS controls. AgNP incorporation impacted bacterial communities by reducing the relative abundance of Flavobacteriaceae (phylum: Bacteroidetes) and increasing the relative abundance of Vibrionaceae (phylum: Proteobacteria) in 28-day-old biofilms compared to PDMS. The settlement rate of M. coruscus on 28-day-old biofilms developed on AgNPs was lower by >30% compared to settlement on control biofilms. Thus, the incorporation of AgNPs influences biofilm bacterial communities in the marine environment and subsequently inhibits mussel settlement.