Cyanobacteria can produce numerous secondary metabolites (cyanotoxins) with various toxicities, yet data on cyanotoxins in many lakes are limited. Moreover, little research is available on complex relations among cyanobacteria that produce toxins. Therefore, we studied cyanobacteria and 19 cyanotoxins at three sites with recurring blooms in Kabetogama Lake (USA). Seven of 19 toxins were detected in various combinations. Anabaenopeptin A and B were detected in every sample. Microcystin-YR was detected more frequently than microcystin-LR, unlike other lakes in the region. Microcystin-YR concentrations, however, generally were low; two samples exceeded drinking water guidelines and no samples exceeded recreational guidelines. Anabaenopeptins correlated with six cyanobacterial taxa, most of which lack available literature on peptide production. The potential toxin producing cyanobacteria, Microcystis, was significantly correlated to microcystin-YR. Pseudanabaena sp. and Synechococcus sp. had strong negative correlations with several toxins that may indicate competition or stress between organisms. Non-metric multidimensional scaling identified three cyanobacterial pairs that may reflect symbiotic or antagonistic relations. This study highlights interactions among cyanobacteria and multiple cyanotoxins and the methods used may be useful for uncovering additional patterns in cyanobacteria communities in other systems, leading to further understanding of how those interactions lead to toxin production.