Data assimilation techniques allow the integration of multi-source data with physical modeling of dense nonaqueous phase liquid (DNAPL) source zones to monitor their evolution in time and thereby improve remediation efforts. The DNAPL source zone is governed by multiphase physics and its architecture is usually highly irregular and nonstationary. Traditional data assimilation methods use stationary models to describe these nonstationary DNAPL saturation fields, leading to significant errors in the estimation of unknown source zone architectures (SZAs). In this study, we propose a geostatistical data assimilation method to improve performance monitoring of DNAPL remediation. We estimate the DNAPL SZA after parameterizing the DNAPL saturation field using a deep learning method instead of a stationary statistical model. First, we train a convolutional variational autoencoder (CVAE) network to capture the physics of DNAPL infiltration and depletion. Then, we incorporate the CVAE network within the Ensemble Kalman filter (EnKF) to resolve the evolving DNAPL SZA by assimilating time-lapse hydrogeophysical measurements (i.e., oscillatory hydraulic tomography, downgradient dissolved DNAPL concentration, and electrical resistivity tomography). To assess the proposed CVAE-EnKF framework's performance, we conducted numerical experiments with evolving DNAPL SZAs in a 2D heterogeneous aquifer. Results show that the proposed framework significantly improved DNAPL saturation estimates throughout the source zone over time, compared to the standard EnKF method. CVAE-EnKF reduced the estimation error of DNAPL mass remediated by 51% from EnKF, along with better predictions of source zone longevity. It also better captured the morphology and center/spread of mass of the evolving remediated portions of the source zone and provided better estimates of pooled-DNAPL mass. Furthermore, the CVAE-EnKF method is more stable and converges faster than EnKF alone. Overall, the proposed data assimilation framework can improve real-time monitoring of DNAPL remediation and risk analysis.