The global spread of parasitic chytrid skin fungi (Batrachochytrium spp.) is a primary cause of amphibian population declines and extinctions. In Europe, Batrachochytrium salamandrivorans (Bsal) has caused significant declines in fire salamander populations and has yet unpredictable impacts on other European caudate species. The infectious stage of Bsal is an aquatic flagellate zoospore with a diameter of approximately 4.5 µm. Daphnia, a filter-feeding microplankton commonly found in amphibian breeding sites, has been demonstrated to consume zoospores of another chytrid fungus, Batrachochytrium dendrobatidis (Bd). In this study, we investigated the capacity of Daphnia magna to consume and digest Bsal zoospores under controlled laboratory conditions. We applied Nile red-stained and unstained zoospores to Daphnia magna and verified consumption visually and via quantitative polymerase chain reaction. Additionally, the daphnids were subjected to a feeding choice experiment with algae Acutodesmus sp. and Bsal zoospores to determine if the presence of a primary food source affects zoospore uptake. Our results demonstrated that the capability of zoospore uptake could not be disturbed by the presence of algae. These findings suggest that a more comprehensive examination of zooplankton communities and their interactions with and potential to regulate aquatic infectious fungi is required to better understand ecosystems with endangered amphibians adequately.