A growth toxicity assay with mixed cultures of cyanobacteria and algae using in vivo fluorescence is presented. Test organisms (the green alga Pseudokirchneriella subcapitata and the cyanobacterium Aphanothece clathrata) growing alone and in a mixture were exposed to selected chemicals. P. subcapitata featured a higher sensitivity to toxicants in the presence of A. clathrata compared to the single species assay. On the other hand, growth of a cyanobacterium was not affected by the presence or absence of the green alga. The proposed method seems to be suitable for pre-screening studies of toxicants (algistatic agents, herbicides) applied into the aquatic environment and for the assessment of their impact on natural phytoplankton communities.