There has been growing interest in incorporating the transient storage effect into modeling solute transport in streams. In particular, for a smaller mountain stream where flow is fast and the flow field is irregular (a favorable environment to induce dead zones along the stream), long tails are normally observed in the stream tracer data, and adding transient storage terms in the advection-dispersion transport equation can result in more accurate simulation. While previous studies on transient storage modeling account for temporary, localized exchange between the stream and the shallow groundwater in the hyporheic zone, largerscale exchange with the groundwater in the underlying aquifer has rarely been included or properly coupled to surface water modeling. In this paper, we complement previous modeling efforts by incorporating the transient storage concept in a conjunctive stream-aquifer model. Three well-documented and widely used USGS models have been coupled to form the core of this conjunctive model: MODFLOW handles the groundwater flow in the aquifer; DAFLOW accurately computes unsteady streamflow by means of the diffusive wave routing technique, as well as stream-aquifer exchange simulated as streambed leakage; and MOC3D computes solute transport in the groundwater zone. In addition, an explicit finite difference package was developed to incorporate the one-dimensional transient storage equations for solute transport in streams. The quadratic upstream interpolation (QUICK) algorithm is employed to improve the accuracy of spatial differencing. An adaptive stepsize control algorithm for the Runge-Kutta method is incorporated to increase overall model efficiency. Results show that the conjunctive stream-aquifer model with transient storage can handle well the bank storage effect under a flooding event. When it is applied over a stream network, the results also show that the stream-aquifer interaction acts as a strong source or sink along the stream and is too significant to be ignored. The adaptive stepsize control for stream solute transport improves overall model performance.