A method and apparatus for monitoring waterbed environment are described. The method may comprise determining a first temperature at a location within the water column of a surface body of water that is representative of the upper thermal boundary condition between surface water and pore water environments, and determining at least a second temperature at the location at a first depth below a waterbed surface. The first and second temperatures are then used to monitor a waterbed environment. Certain embodiments are particularly useful for monitoring spatiotemporal variations of riverbed surface elevations, such as scour and deposition, over a time period. Probe/sensor assemblies are disclosed for practicing the method.