A terrain mapping system is disclosed for use with an excavation machine at a worksite. The terrain mapping system may have a locating device mountable onboard the excavation machine and configured to generate a first signal indicative of a position of the excavation machine at the worksite, and a sensor configured to generate a second signal indicative of a load on the excavation machine. The terrain mapping system may also have a controller in communication with the locating device and the sensor. The controller may be configured to update a surface contour of the worksite contained in an electronic map based on the first signal as the excavation machine traverses the worksite, and to determine an amount of material moved by the excavation machine based on the second signal. The controller may also be configured to generate a representation of the material moved by the excavation machine in the electronic map when the excavation machine ceases to move the material.