The filamentous cyanobacterium Lyngbya wollei (Farlow ex Gomont) comb. nov. forms dark green to black mats on the bottom of rivers and lakes. Benthic mats often remain inconspicuous until they float to the surface because of trapped gas bubbles or until high winds and wave action dislodge and wash mats ashore. Mats induce dark, anoxic conditions conducive to nutrient mineralization, atmospheric N₂ fixation, and heterotrophic metabolism. Lyngbya wollei has been found historically in southeastern USA, but genetically similar subgroups have been proliferating more recently in the Laurentian Great Lakes and the St Lawrence River. This taxon is found under contrasting environmental conditions, including very clear, thermally and chemically stable, and heavily mineralized Florida Springs and turbid, high dissolved organic C, and seasonally variable conditions, influenced by agricultural tributaries in the St Lawrence River. Lyngbya wollei produces a number of unique saxitoxins and volatile organic compounds that are responsible for a musty-earthy taste and odor in water, which affect aesthetics and recreational water uses. Mats of L. wollei are less palatable than other vegetation but provide shelter for invertebrates, which hide in dark mats of filaments. In the St Lawrence River, wetlands dominated by L. wollei tend to be characterized by a lower biomass of invertebrates and large fish, lower fish species richness, and slower-growing juvenile fish than macrophyte-dominated wetlands. Replacement of macrophytes by L. wollei mats induces a shift in trophic structure and coincides with a decrease in carrying capacity for fish, and significantly alters the dynamics of freshwater ecosystems.