Silver nanoparticles (AgNPs) have been assessed to have a high exposure risk for humans and aquatic organisms. Toxicity varies considerably between different types of AgNPs. This study aimed to investigate the toxic effects of AgNPs with different particle sizes (40 and 110 nm) and different surface coatings (sodium citrate and polyvinylpyrrolidone, PVP) on Daphnia magna and their mechanisms of action. The results revealed that the citrate-coated AgNPs were more toxic than PVP-coated AgNPs and that the 40 nm AgNPs were more toxic than the 110 nm AgNPs. Transcriptome analysis further revealed that the toxic effects of AgNPs on D. magna were related to the mechanisms of ion binding and several metabolic pathways, such as the "RNA polymerase" pathway and the "protein digestion and absorption" pathway. Moreover, the principal component analysis (PAC) results found that surface coating was the major factor that determines the toxicities compared to particle size. These results could help us better understand the possible mechanism of AgNP toxicity in aquatic invertebrates at the transcriptome level and establish an important foundation for revealing the broad impacts of nanoparticles on aquatic environments.