The co-occurrence of non-toxic phytoplankton alongside cyanobacteria adds to the challenge of treating source waters with harmful algal blooms. The non-toxic species consume the oxidant and, thereby, reduce the efficacy of oxidation of both the extracellular and intracellular cyanotoxins. In this work, a 3D printed mini-hydrocyclone was used to separate a mixture of non-toxic green algae, Scenedesmus obliquus, from a toxic species of cyanobacteria, Microcystis aeruginosa. When water is pumped through the mini-hydrocyclone, cells exit through an overflow or underflow port depending on their size, shape, and density relative to the other cells and particles in the water matrix. The overflow port contains the cells that are smaller and less dense since these particles move toward the center of the hydrocyclone. In this work, the majority (>93%) of Microcystis cells were found in the overflow while the underflow contained primarily the Scenedesmus (>80%). This level of separation efficiency was maintained over the 30-min experiment and the majority of both cells (>86%) remained viable following the separation, which indicates that the pumping combined with forces exerted within the mini-hydrocyclone were not sufficient to cause cell death. The impact of free chlorine on the cells both pre-separation and post-separation was evaluated at two doses (1 and 2 mg/L). After separation, the overflow, which contained primarily Microcystis, had at least a 24% reduction in the free chlorine decay rate as compared to the feed water, which contained both species. This reduction in chlorine consumption shows that the cells separated via mini-hydrocyclone would likely require lower doses of oxidant to produce a similar level of degradation of the cyanotoxins present in either the extracellular or intracellular form. However, future work should be undertaken to evaluate this effect in natural bloom samples.