Using reclaimed water to irrigate crops can be an important route for organic contaminants of emerging concern (CECs) to be introduced into agricultural production and thus find their way into the food chain. This work aims to establish accumulation models for the different parts of a crop (fruit/leaves/roots) and the soil of some of the most commonly detected CECs in reclaimed water, through field trials in greenhouses. For this, tomato plants were permanently irrigated under realistic agricultural conditions with a mixture of the selected compounds at approx. 1 μg/L. A total of 30 contaminants were analyzed belonging to different compound categories. A modified QuEChERS extraction method followed by liquid chromatography coupled to tandem mass spectrometry was the procedure used. The study revealed the presence of 21 target contaminants in the tomatoes, and 18 CECs in the leaves, roots, and soil. The average total concentration of pesticides detected in the tomatoes was 3 μg/kg f.w., whereas the average total load of pharmaceuticals was 5.8 μg/kg f.w. after three months, at the time of crop harvesting. The levels of pharmaceutical products and pesticides in the non-edible tissues were up to 3.5 and 2.1 μg/kg f.w., respectively, in the leaves and up to 89.3 and 31.3 μg/kg f.w., respectively, in the roots. In the case of the soil samples, the pesticide concentration found after crop harvesting was below 11.4 μg/kg d.w., and less than 3.0 μg/kg d.w. for pharmaceuticals. Overall, the concentration levels of CECs detected in the tomatoes, which were permanently irrigated with contaminated reclaimed water, do not pose a risk to human health via dietary intake. Display omitted •Soil samples exhibited the highest content of CECs followed by fruit ≥ leaf ≥ roots.•We identify CECs with the highest potential for plant uptake and soil accumulation.•We propose mathematical models to estimate the CECs uptake in soil and plants.•A correlation was found between CECs uptake and logKow.•Daily human intake was estimated considering the worst-case scenario.