Toxic cyanobacterial blooms are prevalent in surface waters. Depending on several conditions, these blooms produce cyanotoxins. Human exposure to these toxins can occur through multiple routes, including contaminated crops through irrigation with contaminated water. Analytical methods have been developed for cyanotoxin quantification to investigate these exposures. Yet, proper comparisons between different labs via proficiency tests or interlaboratory comparison tests, as well as method quality assurance, are impossible. Developing reference materials for cyanotoxins in plants would help resolve these problems. Therefore, a novel liquid hydroculture setup was optimized to grow and contaminate strawberries. During fruit ripening, these plants were exposed to growth medium contaminated with pure microcystin-LR or freeze-dried cyanobacterial biomass containing different microcystin congeners. Afterwards, fruits, greens, and roots were harvested. Validated UHPLC-MS/MS methods were used to quantify the microcystin congeners in the growth medium and the plants. Furthermore, both contamination conditions resulted in the accumulation of toxin(s) in the roots and the greens. Yet in the contamination models, no toxin(s) accumulated in the fruits. Therefore, this contamination approach, combined with strawberries as a berry plant model, is only suitable for reference material production for limited matrices. Our cultivation model to produce reference material could be evaluated for other berry producers.