Two algorithms set for automatic detection of bow shock (BS) and magnetopause (MP) boundaries at Saturn using in situ magnetic field and plasma data acquired by the Cassini spacecraft are presented. Traditional threshold-based and modern deep learning algorithms were investigated for the task of boundary detection. Sections of Cassini’s orbits were pre-selected based on empirical BS and MP boundary models, and from outlier detection in magnetic field data using an autoencoder neural network. The threshold method was applied to pre-selected magnetic field and plasma data independently to compute parameters to which a threshold was applied to determine the presence of a boundary. The deep learning method used a type of convolutional neural network (CNN) called ResNet on images of magnetic field time series data and electron energy-time spectrograms to classify the presence of boundaries. 2012 data were held out of the training data to test and compare the algorithms on unseen data. The comparison showed that the CNN method applied to plasma data outperformed the threshold method. A final multiclass CNN classifier trained on plasma data obtained F1 scores of 92.1% ± 1.4% for BS crossings and 84.7% ± 1.9% for MP crossings on a corrected test dataset (from use of a bootstrap method). Reliable automated detection of boundary crossings could enable future spacecraft experiments like the PEP instrument on the upcoming JUICE spacecraft mission to dynamically adapt the best observing mode based on rapid classification of the boundary crossings as soon as it appears, thus yielding higher quality data and improved potential for scientific discovery.