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We present deep learning (DL) networks for three‐dimensional (3D) joint inversion of active seismic full waveform and passive seismic traveltime data to image reservoirs and their properties and quantify imaging uncertainties. Active seismic full‐waveform data can provide high‐resolution monitoring images but are collected only intermittently because of their high acquisition cost. In contrast, passive seismic data can be gathered at relatively low cost between regular active surveys, although their imaging quality can be compromised by factors such as low signal‐to‐noise ratios and limited ray coverage of the target. Although these datasets are routinely acquired together at CO2 storage sites, their combined inversion within a 3D DL framework has not been previously demonstrated. To our knowledge, this is the first study to address this gap, combining the strength of both data types. For efficient data storage and DL training with large 3D seismic datasets, we use a 3D data matrix in which a random number of passive seismic traveltime data are stored as parabolic envelopes using one‐hot encoding and a 3D full‐waveform data matrix in which multiple shot gathers are summed. Two network architectures are evaluated: a single‐encoder U‐Net for single‐data type inversion and a dual‐encoder U‐Net for joint inversion of active and passive seismic data. We also evaluate the single‐encoder U‐Net for joint inversion by concatenating full‐waveform data and traveltime data. We propose a systematic approach for selecting an optimal dropout rate that balances regularization during training and Monte Carlo dropout‐based uncertainty quantification during prediction by examining the correlation coefficient between standard deviation and prediction error, along with the training misfit, across a range of dropout rates. 3D DL inversion experiments include five different network configurations, with evaluations under ideal, noisy and dropout‐enabled conditions. Both model and data uncertainties are assessed, as well as their combined effects. Across all conditions, the networks consistently predict accurate CO2 saturation models with low prediction errors, such as a structural similarity index of 0.993 and CO2 difference of 1.1%. Uncertainty estimates show strong spatial correlation with prediction errors, confirming the effectiveness of the proposed dropout selection approach. The results demonstrate that our DL approach, utilizing compact data representations and appropriate uncertainty quantification, yields accurate subsurface images under various inversion conditions and provides valuable insights into the reliability of predictions.