ABSTRACT This study presents the ‘Dual Path CNN-MLP’, a novel hybrid deep neural network (DNN) architecture that merges the strengths of convolutional neural networks (CNNs) and multilayer perceptrons (MLPs) for regional groundwater flow simulations. This model stands out from previous DNN approaches by managing mixed input types, including both imagery and numerical vectors. Such flexibility allows the diverse nature of groundwater data to be efficiently utilized without the need to convert it into a uniform format, which often leads to oversimplification or unnecessary expansion of the dataset. When applied to the northeast Qatar aquifer, the model demonstrates high accuracy in simulating transient groundwater flow fields, benchmarked against the well-established MODFLOW model. The model's efficacy is confirmed through k-fold cross-validation, showing an error margin of less than 12% across all examined locations. The study also examines the model's ability to perform uncertainty analysis using Monte Carlo simulations, finding that it achieves around 1% average absolute percentage error in estimating the mean hydraulic head. Errors are mostly found in areas with significant variations in the hydraulic head. Switching to this ML model from the conventional MODFLOW simulator boosts computational efficiency by about 99%, showcasing its advantage for tasks like uncertainty analysis in repetitive groundwater simulations.