Cyanobacterial harmful algal blooms (cyanoHABs) are a growing global concern due to their negative impacts on freshwater lakes and river ecosystems. HABs impact local and regional economies by restricting fisheries resources, recreational and commercial waterways, and threatening drinking water sources. To control HABs, researchers are developing short- and long-term mitigation strategies by exploiting natural, bacterial-derived products as targeted chemical control reagents to reduce the severity of HABs. In this study, we characterized the cyanocidal and ecotoxicological properties of tryptoline, tryptamine, isatin and other commercially available, bacterially derived compounds against both lab-adapted and field collected freshwater cyanobacterial strains that collectively include genera from Microcystis, Umezakia, Raphidiopsis, Dolichospermum, Planktothrix, Vulcanococcus, Anabaena and Synechocystis. Initially, chemicals were assessed for their ability to control cyanobacteria by screening them on cyanobacteria lawn plates. Those chemicals that created zones of clearing underwent further testing through liquid assay studies, where biomass was monitored using chlorophyll extractions. Results indicate that tryptoline was the most effective chemical at all concentrations tested leading to a 52 % reduction in algal biomass and this was independent of initial algal biomass, whereas tryptamine reduced algal biomass by 25 % and was most effective at low to medium algal cell densities. In addition, tryptoline was more toxic to the cyanobacteria strains in both the single and repeated exposures compared to tryptamine due to its increased resistance to degradation compared to tryptamine which had degraded 27.9 % after 72 h. The acute and chronic toxicity studies using the standard non-target zooplankton Ceriodaphnia dubia and fish Pimephales promelas resulted in hazard values for tryptoline that indicate it could be difficult to achieve an acceptable margin of safety to avoid non-target species effects when using this chemical in a cyanoHAB treatment. In contrast, tryptamine was at least 2 times less toxic to both non-target species than trypoline (e.g., Pimephales promelas 96-hour LC50 for tryptamine was 26.97 mg/L compared to had an 96-hour LC50 of 2.9 mg/L for tryptoline). Results from these studies collectively provide further data on the feasibility of bacterial-derived algaecides with regards to multi-treatment regimens and optimal cyanobacterial bloom densities. These studies also provide relevant non-target species testing and safety factors for those chemicals demonstrating the most effective algaecide activity.