Cyanobacterial harmful algal blooms (cyanoHABs) are a growing problem in freshwater systems worldwide. CyanoHABs are well documented in Green Bay, Lake Michigan but little is known about cyanoHAB toxicity. This study characterized the diversity and spatial distribution of toxic or otherwise bioactive cyanobacterial peptides (TBPs) in Green Bay. Samples were collected in 2014 and 2015 during three cruises at sites spanning the mouth of the Fox River north to Chambers Island. Nineteen TBPs were analyzed including 11 microcystin (MC) variants, nodularin, three anabaenopeptins, three cyanopeptolins and microginin-690. Of the 19 TBPs, 12 were detected in at least one sample, and 94% of samples had detectable TBPs. The most prevalent TBPs were MCRR and MCLR, present in 94% and 65% of samples. The mean concentration of all TBPs was highest in the Fox River and lower bay, however, the maximum concentration of all TBPs occurred in the same sample north of the lower bay. MCs were positively correlated with chlorophyll and negatively correlated with distance to the Fox River in all cruises along a well-established south-to-north trophic gradient in Green Bay. The mean concentration of MC in the lower bay across all cruises was 3.0 ± 2.3 μg/L. Cyanopeptolins and anabaenopeptins did not trend with the south-north trophic gradient or varied by cruise suggesting their occurrence is driven by different environmental factors. Results from this study provide evidence that trends in TBP concentration differ by congener type over a trophic gradient.