We develop the a posteriori error analysis for a mixed finite element method applied to the coupling of Brinkman and Darcy equations in 3D, modelling the interaction of viscous and non-viscous flow effects across a given interface. The system is formulated in terms of velocity and pressure within the Darcy subdomain, together with vorticity, velocity and pressure of the fluid in the Brinkman region, and a Lagrange multiplier enforcing pressure continuity across the interface. The solvability of a fullymixed formulation along with a priori error bounds for a finite element method have been recently established in Álvarez et al. ( Comput Methods Appl Mech Eng 307:68-95, 2016). Here we derive a residual-based a posteriori error estimator for such a scheme, and prove its reliability exploiting a global inf-sup condition in combination with suitable Helmholtz decompositions, and interpolation properties of Clément and Raviart-Thomas operators. The estimator is also shown to be efficient, following a localisation strategy and appropriate inverse inequalities. We present numerical tests to confirm the features of the estimator and to illustrate the performance of the method in academic and application-oriented problems.