In one aspect, a system for monitoring crop fill-levels of transport receptacles, includes a crop transport receptacle defining a storage volume including at least a first sub-region and a second sub-region. The system also includes first and second fill-level sensors having fields of view directed towards harvested crops contained within the first and second sub-regions of the storage volume, respectively. In addition, the system includes a computing system configured to determine a first fill-level value associated with a fill-level of the first sub-region based on data received from the first fill-level sensor and a second fill-level value associated with a fill-level of the second sub-region based on data received from the second fill-level sensor. The computing system is further configured to determine an estimated fill-level value associated with at least a portion of the storage volume including the sub-regions based on the first and second fill-level values.