The influence of environmental conditions and hydrologic connectivity on cyanobacteria assemblages in two drowned river mouth lakes

► We evaluated cyanotoxins, water chemistry, and cyanobacteria communities. ► Microcystin concentrations were inversely correlated with nitrate. ► Cylindrospermopsis raciborskii did not contain the toxin producing gene. ► Local environmental conditions controlled microcystin concentrations.