The influence of the global warming resulting from climate change (CC) together with the presence of freshwater toxins has led to many risks for different water uses and human health. The present chapter discussed the potential risks associated with the effect of global warming on the diffusion of freshwater toxins into the production of drinking water and its impact on the transmission of water-borne diseases affecting human health and other aquatic organisms. Freshwater toxins were classified into algal toxins (cyanotoxins) and fungal toxins (mycotoxins). Cyanotoxins were classified into cyclic peptides (microcystins (MCs)) having different chemical compounds. These are attributed to the variability of their characteristic function. Cyanobacterial toxins may lead to instability of the health of aquatic ecosystems and should not be ignored with their specific harmful effects. Fungal toxins (mycotoxins) were also considered natural toxins coinciding with the prediction of climate change scenarios, which may affect human health and the ecosystem. The adverse effects of freshwater toxins on human health and the aquatic environment were illustrated. The harmful algal bloom (HAB) toxins have acute and chronic health consequences in mammals (including humans) and aquatic organisms. Mycotoxins negatively affect aquatic organisms and animal and human health. Regarding the detection methods of freshwater toxins, various traditional analytical methods were reported for the detection of cyanotoxins, including high-performance liquid chromatography (HPLC), protein phosphatase inhibition assay (PPIA), and enzyme-linked immunosorbent assay (ELISA). It is important to realize the natural toxins in an engagement in climate policy plans, planning, and action. Mitigation and adaptation efforts should be focused on surveillance schedules, more laws, and comprehension of the toxicity of the toxic substances.