Cyanobacteria, ancient prokaryotes, interfere with ecosystem water quality through the production of cyanotoxins and bloom formation. Therefore, for water safety and public health reasons, the application of faster, sensitive, and specific tools on its risk assessment is demanded. Polymerase chain reaction (PCR) coupled with DNA sequencing can be a helpful tool for the presence and potential to cyanotoxicity. To achieve these, seven waterbodies located on the North and Center regions of Portugal were sampled for two monitoring periods (2017 and 2018). Thus, given the five risk levels proposed (none up to four cyanotoxins - mcyA, cyrC, anaC, sxtI - being detected per risk level), results showed that the great majority of the ecosystems analyzed on the presence of blooms and under climate change phenomenon (heat waves) had an elevated risk (up to four cyanotoxins being detected) corresponding to a situation of high potential of cyanotoxicity. In the opposite conditions (i.e., absence of blooms and heat waves), the risk was lowered to none or only one cyanotoxin being detected. Two ecosystems escaped this trend and demonstrated little to no alterations among risk levels from 1 year to another corresponding to a high potential of cyanotoxicity and cyanotoxins persistence in comparison to other studied ecosystems. Overall, the risk assessment undertaken suggests that other ecosystems ecological variables (physical, hydrological, or chemical) are interfering on the occurrence and persistence of cyanotoxins biosynthesis genes. Given the observed conditions (eutrophic status, bloom occurrence, and heat waves) of the analyzed ecosystems, cyanobacterial potential for toxicity seems to have increased, suggesting a need of the incorporation of other cyanotoxins apart of the regulated microcystins-LR on cyanotoxins surveillance programs of Portugal.