The potential transfer of microcystin-LR (MC-LR) to humans via crop plants irrigated with MC-contaminated water is causing serious concern. In this study, two Oryza sativa variants, a hybrid (BG358), a traditional (Suwandel) variety, and a leafy green vegetable crop, Ipomoea aquatica, were exposed under laboratory conditions to natural blooms of Microcystis aeruginosa sampled from a hypereutrophic lake contaminated with MC-LR (3,197.37 ± 1.04 µg/L). Field samples of O. sativa and I. aquatica were collected from farmlands that had been irrigated from a reservoir, containing MC-LR (180 µg/L). MC-LR was quantified by high performance liquid chromatography followed by photodiode-array detection (HPLC-PDA). From the laboratory study, we calculated the potential human health exposure from BG358, Suwandel and I. aquatica as 2.84 ± 0.01, 0.22 ± 0.01, and 0.06 ± 0.01 µg/kg of body weight/day, respectively, whereas the potential health exposures from BG358, Suwandel and I. aquatica collected from the field were 0.10 ± 0.01, 0.009 ± 0.005, and 0.03 ± 0.01 µg/kg of body weight/day, respectively. In certain instances, the results exceeded the World Health Organization’s (WHO) tolerable daily intake of MC-LR, posing a potential health risk to humans. Thus, our results emphasize the importance of continuous screening programs for cyanotoxins in edible plants in the future to prevent the consumption of contaminated crops.