Introduction: Cyanobacteria are found worldwide and can produce cyanotoxins. Since homeopathic potencies can modulate toxicity in different biological models, this study proposes to investigate whether cyanobacteria toxins might also be the case. Objectives: a) to investigate if homeopathic potencies can improve the resilience of Artemia franciscana (brine shrimp) embryos to saxitoxin (cyanotoxin) and to control the growth of Raphidiopsis raciborskii in vitro; b) to verify if physicochemical parameters can be used to track homeopathic potencies in seawater or cyanobacteria medium, with special focus on the interaction with solvatochromic dyes. Method: Artemia franciscana cysts were cultivated in seawater in 96-well plates to evaluate the hatching rate, vitality, and gene expression of heat shock proteins (Hsp), after being challenged with R. raciborskii extract containing 2.5 µg/liter of saxitoxin and treated with different homeopathic potencies chosen from a screening process. Cultures of R. raciborskii maintained in ASM-1 medium were equally treated with previously screened homeopathic potencies, and their growth was monitored as a function of time. The physicochemical properties of treated water were evaluated by interacting with solvatochromic dyes and measuring pH, conductivity, and temperature. Results: A lower rate of hatching of Artemia franciscana cysts was observed after treatment with Nitric acidum 6cH (p=0.03), and a complete toxicity reversal with increased Hsp 26 and p26 gene expression was seen after treatment with Isotherapic (R. raciborskii extract) 200cH (p≤0.02). Nitric acidum 200cH and Mercurius solubilis 30cH limited the exponential growth of cyanobacteria (p≤0.003) regardless of their concentration. Coumarin 7 was a marker for Nitric acidum 6cH and Isotherapic (R. raciborskii extract) 200cH, even when inserted into seawater. Nile red was a marker for Nitric acidum 200cH and Mercurius solubilis 30cH, even when inserted into ASM-1 medium (p≤0.05). An increase in pH and endo/exothermal effects of the ASM-1 medium was observed after these treatments (p≤0.007). The physicochemical analyzes were optimized after the previous submission of the samples to a constant unidirectional 2400 Gauss magnetic flow. Conclusion: The Isotherapic 200cH improved Artemia franciscana bioresilience to saxitoxin itself; Nitric acidum 200cH and Mercurius solubilis 30cH limited the growth of R. raciborskii. In all cases, those homeopathic potencies that showed biological effects were traceable in the aqueous medium using solvatochromic dyes, especially when the samples were subjected to the magnetic field.