Quantum transmission links are central elements in essentially all implementations of quantum information protocols. Emerging progress in quantum technologies involving such links needs to be accompanied by appropriate certification tools. In adversarial scenarios, a certification method can be vulnerable to attacks if too much trust is placed on the underlying system. Here, we propose a protocol in a device independent framework, which allows for the certification of practical quantum transmission links in scenarios where minimal assumptions are made about the functioning of the certification setup. In particular, we take unavoidable transmission losses into account by modeling the link as a completely-positive trace-decreasing map. We also, crucially, remove the assumption of independent and identically distributed samples, which is known to be incompatible with adversarial settings. Finally, in view of the use of the certified transmitted states for follow-up applications, our protocol moves beyond certification of the channel to allow us to estimate the quality of the transmitted state itself. To illustrate the practical relevance and the feasibility of our protocol with currently available technology we provide an experimental implementation based on a state-of-the-art polarization entangled photon pair source in a Sagnac configuration and analyze its robustness for realistic losses and errors.