Wireless underground sensor networks (WUSNs) enable many applications such as underground pipeline monitoring, power grid maintenance, mine disaster prevention, and oil upstream monitoring among many others. While the classical electromagnetic waves do not work well in WUSNs, the magnetic induction (MI) propagation technique provides constant channel conditions via small size of antenna coils in the underground environments. In this paper, instead of adopting currently layered protocols approach, a distributed cross-layer protocol design is proposed for MI-based WUSNs. First, a detailed overview is given for different communication functionalities from physical to network layers as well as the QoS requirements of applications. Utilizing the interactions of different layer functionalities, a distributed environment-aware protocol, called DEAP, is then developed to satisfy statistical QoS guarantees and achieve both optimal energy savings and throughput gain concurrently. Simulations confirm that the proposed cross-layer protocol achieves significant energy savings, high throughput efficiency and dependable MI communication for WUSNs.