the date of receipt and acceptance should be inserted later Abstract Accurately mapping the course and vegetation along a river is challenging, since overhanging trees block GPS at ground level and occlude the shore line when viewed from higher altitudes. We present a multimodal perception system for the active exploration and mapping of a river from a small rotorcraft. We describe three key components that use computer vision, laser scanning, inertial sensing and intermittant GPS to estimate the motion of the rotorcraft, detect the river without a prior map, and create a 3D map of the riverine environment. Our hardware and software approach is cognizant of the need to perform multi-kilometer missions below tree level with size, weight and power constraints. We present experimental results along a 2km loop of river using a surrogate perception payload. Overall we can build an accurate 3D obstacle map and a 2D map of the river course and width from light onboard sensing.