Harmful algal blooms (HABs) can contain toxins, like microcystins (MC) produced by Microcystis aeruginosa and other species, that have serious implications for human health. Plants can take up many algal toxins, which can accumulate in their tissues (e.g., when irrigated with HAB water). Since the mechanism of uptake and transport of algal toxins in plants is not understood, we investigated the uptake of MC in tomato. Soil-grown tomatoes (4 adult leaves) irrigated with M. aeruginosa-contaminated nutrient solution had lower biomass compared to plants receiving only nutrient solution, indicating uptake of toxin by roots. Then, we treated similar-sized tomatoes for five days in hydroponic nutrient solutions each lacking one of five forms of N (1 mM urea, glycine, NO3, NH4, and a peptide mix) in solution with 200 µg/L MC-LR. We found no significant differences in MC-LR uptake among N treatments, indicating that the major N-uptake proteins were not responsible for MC-LR uptake into roots. Next, we grew tomatoes hydroponically over a range of MC-LR concentrations (0, 10, 100, 250, 500, and 1000 µg/L), and found that MC-LR uptake rate per g root scaled with toxin concentration, indicating that uptake is via diffusion. These results suggest that strategies to improve plant tolerance to algal toxins might focus on traits that limit general root diffusion-uptake pathways, rather than specific uptake proteins.