Cyanotoxins are potent toxic compounds produced by cyanobacteria during algal blooms, which threaten drinking water supplies. These compounds can poison and kill animals and humans. The host-guest interactions of α-, β-, and γ-cyclodextrins (CD) with problematic cyanotoxins, including microcystins (MCs) and nodularin (NOD), were investigated to demonstrate the potential application of CDs for the removal of these toxins from drinking water or applications related to their separation or purification. MCs and NOD have a hydrophobic Adda chain, which contains diene and benzene functional groups. The complexation of these cyanotoxins with CDs was monitored by nuclear magnetic resonance (NMR). The (1)H NMR spectra for MCs are unchanged upon addition of α-CD (smallest host). However, addition of larger hosts, β-CD and γ-CD, leads to significant changes in chemical shifts of the benzene and diene resonances on the 3-amino-9-methoxy-2,6,8-trimethal-10-phenyldeca-4,6-dienoic acid (Adda) chain of MCs and NOD. Solution pH, natural organic matter, and salinity do not appreciably influence the host-guest complexation under our experimental conditions. The experimental binding constants for MCs and NOD with γ-CD are relatively strong, ranging from 1155 to 507 M(-1). The observed changes in chemical shifts for specific protons and competitive binding experiments demonstrate a 1:1 inclusion complex between γ-CD and MCs or NOD, with the Adda chains threading through the CD ring, resulting in an inclusion complex. Our results suggest that CD-type substrates are useful hosts for the complexation of MCs and NOD. CDs can be readily attached to a number of polymeric or solid supports and their functionality tailored to strengthen specific host-guest interactions. With further development of such materials, CD host-guest chemistry may find direct application in the removal and/or separation science of these compounds.