Aquatic ecosystems are receiving various harmful effects due to anthropogenic chemical pollutions. To protect wildlife, risk assessments of the chemicals are conducted using reference indexes of toxicity estimated by species-level laboratory tests and/or micro-/mesocosm community-level studies. However, the existing micro-/mesocosm communities are structurally too complicated, and it is also difficult to compare the experimental results directly with those from species-level tests. Here, we developed a procedure of a simple bi-trophic microcosm experiment which contains the common species (a green algae, Pseudokirchneriella subcapitata and a cladoceran, Daphnia magna) for testing chemical toxicities. For the proper operation of bitrophic microcosm experiment, the minimum required concentration of primary producer (P. subcapitata) is 5×105 cells mL-1. The microcosm system showed higher stability when the initially introduced D. magna population was composed of neonates (<24-h old) than adults and those mixture. This simple microcosm system would be an applicable tool to estimate the disturbing impacts of pollutants on plant-herbivore interactions, and linking the species- and population-/community level risk assessments in the future studies.