The magnitude and frequency of cyanobacteria harmful algae blooms (cHABs) are increasing on a global scale. Anthropogenic nutrient enrichment, and climate change are drivers of bloom formation and favour cyanobacterial dominance in most aquatic ecosystems. The release of cyanotoxin mixtures by blooms into aquatic systems pose a risk to public and ecosystem health.The majority of cyanotoxin research has focused on specific groups: microcystins (MCs), cylindrospermopsins (CYNs), BMAA, saxitoxins (STXs) (anatoxins) ATXs. Other bioactive cyanopeptides (CNPs) produced by cHABs have received much less attention. The chemistry, toxicology, and environmental concentrations of the anabaenopeptin (APs), cyanopeptolin (CPs), microginin (MGs), cyanobactin (CBs), aeruginosin (ASs) CNP groups are largely unknown despite having notable biological activities and documented co-occurrence with cyanotoxins. Untargeted, targeted, and semi-targeted mass-spectrometry based metabolomic approaches were applied to study the CNP profiles of fifty-five cyanobacteria bloom samples collected from fifteen watercourses in Eastern Ontario and Western Quebec. 117 unique cyanopeptides were identified and ninety-four quantitated. MCs and ferintoic acid A (FA A) were quantified with reference materials and other CNPs were determined semi-quantitatively. CPs and APs displayed the greatest diversity in group variants and possessed similar concentrations and occurrence to that of MCs. Based on environmental concentrations and ubiquity of the CP and AP groups, they are recommended for prioritization in future toxicological and environmental research. Additionally, the apparent rise in cHABs, has drawn attention from paleolimnological researchers. Historical records of cHABs are limited, and proxies of cyanobacteria occurrence are typically restricted to pigments and DNA -both of which are sensitive to environmental degradation. However, MCs produced by freshwater cyanobacteria are stable cyclic hexapeptides. MCs in lake sediment archives can provide context to both the occurrence and toxicity of historical cHABs. To evaluate the use of MCs as a paleolimnological proxy, an MC extraction and quantitation method was iii developed and validated for four MC congeners (MR RR, MC LR, [Dha 7 ]MC LR, MC LA) in lake sediments. The method was applied to sediment cores collected from the Rideau Canal system.The MC method was combined with multiple proxies of Itrax-XRF, chlorophyll-a analyses and radioscopic dating methods to develop a chronology of historical lake conditions. The multi-proxy approach provided a clear indication of increasing biological productivity towards the surface of both cores. The apparent trend of productivity appears to be a result of climate warming and anthropogenic nutrient enrichment. I would like to extend my upmost gratitude and thanks to my supervisor, David McMullin, for the continued guidance and support, and providing the opportunity to develop and expand my chemistry skillset with natural products and cyanobacteria metabolites. ...