We define an error indicator for mixed mortar formulation of flow in porous media. The mixed mortar domain decomposition method for single-phase flow problems was defined by Arbogast et al; it relies on coupling of subdomain problems using mortar Lagrange multipliers defined as continuous piecewise linears on the subdomain interface. The accuracy and efficiency of the resulting interface formulation depends on the number of mortar degrees of freedom which we propose to adapt using error indicators involving jump of the flux across the interface. Rigorous a-posteriori analysis and proof of reliability of the estimator are established for single-phase 2D flow problems with diagonal coefficients for $\rm{RT}_{[0]}$ spaces on rectangular grids. Computational experiments demonstrate the application of the estimator. Next, the algorithm and indicator are extended to the two-phase flow case which is illustrated with numerical examples. We focus on adapting the mortar grid while keeping subdomain grid fixed. Full mortar adaptivity is discussed elsewhere.