Hydraulic conductivity distribution and plume initial source condition are two important factors affecting solute transport in heterogeneous media. Since hydraulic conductivity can only be measured at limited locations in a field, its spatial distribution in a complex heterogeneous medium is generally uncertain. In many groundwater contamination sites, transport initial conditions are generally unknown, as plume distributions are available only after the contaminations occurred. In this study, a data assimilation method is developed for calibrating a hydraulic conductivity field and improving solute transport prediction with unknown initial solute source condition. Ensemble Kalman filter (EnKF) is used to update the model parameter (i.e., hydraulic conductivity) and state variables (hydraulic head and solute concentration), when data are available. Twodimensional numerical experiments are designed to assess the performance of the EnKF method on data assimilation for solute transport prediction. The study results indicate that the EnKF method can significantly improve the estimation of the hydraulic conductivity distribution and solute transport prediction by assimilating hydraulic head measurements with a known solute initial condition. When solute source is unknown, solute prediction by assimilating continuous measurements of solute concentration at a few points in the plume well captures the plume evolution downstream of the measurement points.