This study investigated how giant viruses and their virophages affect the photosynthetic physiology of a freshwater eukaryotic algae, Chrysochromulina parva. The impact of infections with the virus CpV-BQ3 and its associated virophage CpVV-Moe on C. parva photosynthesis were examined using a LI-COR LI-6800® aquatic chamber to simultaneously estimate carbon assimilation and various chlorophyll fluorescence parameters. Results demonstrated that BQ3 inhibited carbon assimilation and decreased Fv/Fm and ΦPSII, indicators of algal culture health and photosynthetic efficiency. Furthermore, this study demonstrated that Moe may mitigate the decrease in carbon assimilation and photosynthetic efficiency experienced by C. parva during infections with BQ3 alone, but these protective effects were observed only at low concentrations of BQ3 and require further investigation. This study opens the door to further research on the physiological influence of this, and other, tripartite infection systems, as well as the role of viral infection dynamics on aquatic ecosystem functioning and metabolism.M.Sc