Uncertainty in the mass flux for advection dominated solute movement in heterogeneous porous media is investigated using the Lagrangian framework developed in paper 1 by Dagan et al. (this issue). Expressions for the covariance of the mass flux and cumulative mass flux are derived as functions of the injection volume and sampling area size relative to the scale of heterogeneity. The result is illustrated for solute advection in three types of heterogeneous porous media: stratified formations, two‐ and three‐dimensional porous media; small perturbation approximation is used for the two‐ and three‐dimensional cases. Variances of the mass flux and cumulative mass flux are evaluated as functions of the injection volume (area) scale versus log‐hydraulic conductivity integral scale. The greatest decrease in coefficient of variation (CV) of the mass flux is for the source scale 1–5 times the hydraulic conductivity integral scale; further increase in the source size decreases CV comparatively less. The variance of the cumulative mass flux (or total discharge) indicates that for the source size of 20 hydraulic conductivity integral scales, the transport conditions are almost ergodic. The present results also indicate that the cumulative mass flux is a relatively robust quantity for describing field‐scale solute transport.