So far, potential chronic risks of silver nanoparticles (AgNPs) on organisms remain largely unknown, especially molecular-level alterations at the environmentally relevant concentrations. In this study, Chlamydomonas reinhardtii (C. reinhardtii) is used as the model organism to investigate chronic toxic effects of 100 μg/L and 50 mg/L AgNPs for 120 d. Physiological studies showed that AgNPs attached on cell surface and internalized into algal cells, inducing the increase in cell permeability, the decline in cell size and granularity, the damage in photosynthetic systems, and the production of reactive oxygen species (ROS). The damage in photosynthetic systems was reflected in the decline in the photosynthetic activity (F