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Accurate prediction of the uptake and translocation of emerging contaminants in plants has serious implications for assessing impacts on ecosystems and human health. However, traditional modeling approaches are not reliable in the prediction of transpiration stream concentration factor (TSCF) and root concentration factor (RCF). This study applied deep neural networks (DNN), recurrent neural networks (RNN), and long short-term memory (LSTM) to enhance the accuracy of predictive models for TSCF and RCF. The predictions and feature importance analysis were based on nine chemical properties and two plant root macromolecular compositions. The results indicated that deep learning models predict TSCF and RCF with improved accuracy compared to mechanistic models. The coefficient of determination (R^2) for the DNN, RNN, and LSTM models in predicting TSCF was 0.62, 0.67, and 0.56, respectively. The corresponding mean squared error (MSE) on the test set for the models was 0.055, 0.035, and 0.06, respectively. The R^2 for the DNN, RNN, and LSTM models in predicting RCF was 0.90, 0.91, and 0.84, respectively. The corresponding MSE for the models was 0.124, 0.071, and 0.126, respectively. The results of feature extraction using extreme gradient boosting underlined the importance of lipophilicity and root lipid fraction.