Copper (Cu2+) is an essential micronutrient for cyanobacteria, but it has a toxic effect above a certain threshold. The presence of Cu2+ in water is usually related to human activity due to it being used in pesticides, fertilizer, and algaecides. Previous studies observed that high Cu2+ concentrations stimulated toxin synthesis in cyanobacteria and microalgae. Furthermore, saxitoxins (STXs) can bind to Cu2+ transporters in microorganisms, decreasing the Cu2+ uptake and consequently reducing Cu toxicity. Therefore, considering the invasive capacity of the cyanobacterium Raphidiopsis raciborskii and its potential for STXs production, this study aimed to evaluate the effects of different Cu2+ concentrations in the production of STXs and growth of R. raciborskii. In acclimatized growth conditions, cultures of R. raciborskii strain (ITUC01) were exposed to four different copper concentrations for 20 days (0.8, 8, 80, and 800 × 10−3 μmol L−1 of CuCl2). Raphidiopsis raciborskii growth and physiological responses were evaluated measuring the cell concentration, cell volume, biovolume, chlorophyll a levels, and STXs concentration. Comparing the lowest and highest Cu2+ concentration (0.8 and 800 × 10−3 μmol L−1), it was observed that the increment of Cu2+ in the medium led to a reduced maximum growth rate (μmax), cell concentration, biovolume, and chlorophyll a levels, while the cell volume increased. Despite the low cell concentration and biovolume in the highest Cu2+ condition, it was observed that the STXs volumetric concentration was significantly high on day 5, which is indicative of the fact that increased Cu2+ concentration might induce STXs production in early growth. In addition, our results revealed that STXs production was uncoupled with growth and a reduction of R. raciborskii toxicity from day 5 to 20 was observed. Therefore, the present study identified some of the survival responses of R. raciborskii in Cu-stressed condition and suggested that Cu2+ might be one of the factors that can affect R. raciborskii bloom toxicity.