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We study the problem of bipedal robot navigation in complex environments with uncertain and rough terrain. In particular, we consider a scenario in which the robot is expected to reach a desired goal location by traversing an environment with uncertain terrain elevation. Such terrain uncertainties induce not only untraversable regions but also robot motion perturbations. Thus, the problems of terrain mapping and locomotion stability are intertwined. We evaluate three different kernels for Gaussian process (GP) regression to learn the terrain elevation. We also learn the motion deviation resulting from both the terrain as well as the discrepancy between the reduced-order Prismatic Inverted Pendulum Model used for planning and the full-order locomotion dynamics. We propose a hierarchical locomotion-dynamics-aware sampling-based navigation planner. The global navigation planner plans a series of local waypoints to reach the desired goal locations while respecting locomotion stability constraints. Then, a local navigation planner is used to generate a sequence of dynamically feasible footsteps to reach local waypoints. We develop a novel trajectory evaluation metric to minimize motion deviation and maximize information gain of the terrain elevation map. We evaluate the efficacy of our planning framework on Digit bipedal robot simulation in MuJoCo., Comment: 10 pages, 10 figures