Removal of cyanobacteria from the water column using a coagulant and a ballast compound is a promising technique to mitigate nuisance. As coagulant the organic, biodegradable polymer chitosan has been promoted. Results in this study show that elevated pH, as may be common during cyanobacterial blooms, as well as high alkalinity may hamper the coagulation of chitosan and thus impair its ability to effectively remove positively buoyant cyanobacteria from the water column. The underlying mechanism is likely a shielding of the protonated groups by anions. Inasmuch as there are many chitosan formulations, thorough testing of each chitosan prior to its application is essential. Results obtained in glass tubes were similar to those from standard jar tests demonstrating that glass tube tests can be used for testing effects of coagulants and ballasts in cyanobacteria removal whilst allowing far more replicates. There was no relation between zeta potential and precipitated cyanobacteria. Given the well-known antibacterial activity of chitosan and recent findings of anti-cyanobacterial effects, pre-application tests are needed to decipher if chitosan may cause cell leakage of cyanotoxins. Efficiency- and side-effect testing are crucial for water managers to determine if the selected approach can be used in tailor-made interventions to control cyanobacterial blooms and to mitigate eutrophication.