A transponder-bonded receiver system with clock recovery may include memory an and one or more processors coupled to the memory and configured to execute one or more program modules to perform: receiving multiple data streams each including a number of data packets, and a number of marker packets with embedded bonding clock references (BCRs) and including marker packet information; adjusting arrival-time-stamps (ATSs) of the marker packets by using the BCRs and including capturing timing between the marker packets based on a local free running counter of the receiver; and determining an adjusted ATS corresponding to an ATS at the receiver for each of the plurality of packets using the ATS and a delta-ATS.