Developing models to assess the nutrient status of plants at various growth stages is challenging due to the dynamic nature of plant development. Hence, this study encoded spatiotemporal information of plants within a single time-series model to precisely assess the nutrient status of aquaponically cultivated lettuce. In particular, the long short-term memory (LSTM) and deep autoencoder (DAE) approaches were combined to classify aquaponically grown lettuce plants according to their nutrient status. The proposed approach was validated using extensive sequential hyperspectral reflectance measurements acquired from lettuce leaves at different growth stages across the growing season. A DAE was used to extract distinct features from each sequential spectral dataset time step. These features were used as input to an LSTM model to classify lettuce grown across a gradient of nutrient levels. The results demonstrated that the LSTM outperformed the convolutional neural network (CNN) and multi-class support vector machine (MCSVM) approaches. Also, features selected by the DAE showed better performance compared to features extracted using both genetic algorithms (GAs) and sequential forward selection (SFS). The hybridization of deep autoencoder and long short-term memory (DAE-LSTM) obtained the highest overall classification accuracy of 94%. The suggested methodology presents a pathway to automating the process of nutrient status diagnosis throughout the entire plant life cycle, with the LSTM technique poised to assume a pivotal role in forthcoming time-series analyses for precision agriculture.