During probabilistic analysis of flow and transport in porous media, the uncertainty due to spatial heterogeneity of governing parameters are often taken into account. The randomness in the source conditions also play a major role on the stochastic behavior in distribution of the dependent variable. The present paper is focused on studying the effect of both uncertainty in the governing system parameters as well as the input source conditions. Under such circumstances, a method is proposed which combines with stochastic finite element method (SFEM) and is illustrated for probabilistic analysis of concentration distribution in a 3-D heterogeneous porous media under the influence of random source condition. In the first step SFEM used for probabilistic solution due to spatial heterogeneity of governing parameters for a unit source pulse. Further, the results from the unit source pulse case have been used for the analysis of multiple pulse case using the numerical convolution when the source condition is a random process. The source condition is modeled as a discrete release of random amount of masses at fixed intervals of time. The mean and standard deviation of concentration is compared for the deterministic and the stochastic system scenarios as well as for different values of system parameters. The effect of uncertainty of source condition is also demonstrated in terms of mean and standard deviation of concentration at various locations in the domain.