Silver nanoparticles (AgNPs) including a mix of intact nanoparticle-Ag and ‘free’ Ag+ pose high risks to benthic photoautotrophs, but the photosynthetic responses of benthic microbial aggregates to AgNPs still remain largely unknown. Here, periphyton and Nostoc were used to elucidate the photosynthetic responses of benthic algae community to intact nanoparticle-Ag and Ag+. During exposure, both intact nanoparticle-Ag and Ag+ imposed negative effects on photosynthesis of benthic algae, but via different pathways. Specifically, Ag+ had stronger effects on damaging the oxygen-evolving complex (OEC) and thylakoid membrane than intact nanoparticle-Ag. Ag+ also suppressed electron transfer from QA to QB, and impaired phycobilisome. Intact nanoparticle-Ag inhibited the expression of PsbD and PsbL in PSII, but prompted the ROS scavenging capacity. In response to the stress of AgNPs, the benthic algae increased light energy absorption to maintain the electron transport efficiency, and up-regulated PSI reaction center protein (PsaA) to compensate the degraded PSII. These results reveal how intact nanoparticle-Ag and Ag+ influence electron transport, energy conversion and protein expression in the photosynthesis of periphyton, and provide deep insights into the responses of benthic photoautotrophs to different components of AgNPs.