The magnitude and frequency of cyanobacteria harmful algae blooms is increasing on a global scale. The majority of cyanotoxin research has focused on specific groups: microcystins, cylindrospermopsin, saxitoxins, and anatoxins. Other bioactive cyanopeptides (CNPs) produced by cABs have received much less attention. The chemistry, toxicology, and environmental concentrations of other CNP groups are largely unknown despite having notable biological activities. Mass-spectrometry based metabolomic approaches were applied to study the CNP profiles of fifty-five bloom samples collected from nineteen freshwater watercourses. Based on environmental concentrations and ubiquity of the CP and AP groups, they are recommended for prioritization in future toxicological and environmental research. Additionally, historical records of cyanobacteria bloom are limited. An analytical method for quantitation of MCs in Lake sediments was developed and validated. The method was applied with multi-proxy paleolimnological analyses and radioistope dating methods to evaluate lake sediment cores archives in the Rideau Canal system.