Microcystin-LR (MC-LR) is one of the most toxic and common microcystins (MCs) variant found in aquatic ecosystems. Little is known about the possibility of recovering microcystins contaminated agricultural crops. The objectives of this study were to determine the bioaccumulation and depuration kinetics of MC-LR in leaf tissues of lettuce and arugula, and estimate the total daily intake (ToDI) of MC-LR via contaminated vegetables by humans. Arugula and lettuce were irrigated with contaminated water having 5 and 10 μg L− 1 of MC-LR for 7 days (bioaccumulation), and subsequently, with uncontaminated water for 7 days (depuration). Quantification of MC-LR was performed by LC-MS/MS. The one-compartment biokinetic model was employed for MC-LR bioaccumulation and depuration data analysis. MC-LR was only accumulated in lettuce. After 7 days of irrigation with uncontaminated water, over 25% of accumulated MC-LR was still retained in leaf tissues of plants treated with 10 μg L− 1 MC-LR. Total daily toxin intake by adult consumers (60 kg-bw) exceeded the 0.04 μg MC-LR kg− 1 limit recommended by WHO. Bioaccumulation was found to be linearly proportional to the exposure concentration of the toxin, increasing over time; and estimated to become saturated after 30 days of uninterrupted exposure. On the other hand, MC-LR depuration was less efficient at higher exposure concentrations. This is because biokinetic half-life calculations gave 2.9 and 3.7 days for 5 and 10 μg L− 1 MC-LR treatments, which means 29–37 days are required to eliminate the toxin. For the first time, our results demonstrated the possibility of MC-LR decontamination of lettuce plants.