Many questions about the role of planktonic organisms remain unanswered because of the difficulty in obtaining a medium where bacteria and fungi are not present. Moreover, an excess load of these microorganisms in phytoplankton cultures and zooplankton organisms may cause nutrient competition or diseases and consequently the death of the organisms of interest. For this reason, we reviewed several methods that have been used to obtain axenic planktonic cultures through specific metabolic inhibitors, such as antibiotics and antifungal agents. From 1940 to 2016, most research was related to microalgae and crustacean’s cultures, with the antimicrobials: penicillin, streptomycin, chloramphenicol, oxytetracycline, neomycin and nystatin being the most frequently used. The studies that applied antimicrobials agents to planktonic cultures were mainly focused on being able to culture them and to answer questions about the role of bacteria in aquatic communities without previous testing their effectiveness or their effects on non-target organisms. Therefore, this review sought to determine the correct use of antimicrobials in cultures of planktonic organisms to prevent bacterial and fungal growth, without causing damage to non-target organisms and may assist in the implementation of ecologically-oriented scientific experiments where bacterial and/or fungal inhibition is necessary.