The adverse effects of exposure to microcystins in terrestrial crops have been well documented. However, the retention and bioavailability of microcystin-LR, one of the most prevalent cyanotoxins, from soil to plants, is poorly understood. In the present study, the amount of free microcystin-LR from two soil types, a silty sand and clayey loam, with exposure to three toxin concentrations and time was investigated. Using the two soil types, the effects on Medicago sativa (Alfalfa) growth after microcystin-LR exposure via irrigation with spiked water and pre-spiked soil was investigated and the amount of microcystin-LR taken up by the plant quantified. After 3 weeks of growth, the amount of free microcystin-LR remaining in the two soil types with each treatment was quantified. The results indicated that in clayey loam more microcystin-LR is bound to the soil. However, the growth of Alfalfa was only affected in the clayey loam with microcystin/LR exposure via irrigation. Nevertheless, microcystin-LR was detected in Alfalfa grown in both soil types exposed by both irrigation and via pre-spiked soil. Interestingly, more microcystin-LR remained in the silty sand after 3 weeks; yet, more microcystin-LR was taken up by the Alfalfa grown in the silty sand, with a larger concentration in the roots compared to the shoots. The results indicate that the soil type substantially influences the bioavailability and uptake of microcystin-LR and present some insight into the ecological risk posed by microcystin-LR.