Hazardous algal blooms can generate toxic compounds with significant health impacts for exposed communities. The ubiquitous class of algal toxins known as microcystins exhibits significant heterogeneity in its peptide structure, which has been minimally studied, given the significant impact this has on hydrophobicity, acid/base character and related environmental fate and health effects. Octanol–water partition coefficients for the microcystin congeners MCLR, MCRR, MCLY, MCLF, and MCLA were calculated over an environmentally and physiologically relevant pH range. Microcystin-LR log(Kow) partition coefficient values were found to be consistent with previously established literature values, 1.67 to −1.41 between pH 1 and 8. Microcystin RR was found to be pH insensitive with a log(Kow) of −0.7. The remaining congeners exhibit similar pH dependence as MCLR, with systematic increases in hydrophobicity driven by the introduction of more hydrophobic residues to their variable amino acid region. The variation in pH dependent hydrophobicity suggests increased propensity for bioaccumulation and alternate environmental fates for differing microcystin forms, requiring further investigation.