We propose a combined transport – medium access control (MAC) layer scheme to provide relative service differentiation to Transmission Control Protocol (TCP) flows over a geostationary (GEO) bandwidth on demand (BoD) satellite networks. Our approach involves the joint configuration of TCP-Performance Enhancing Proxy (TCP-PEP) agents at the transport layer and the scheduling algorithm controlling the resource allocation at the MAC layer. The scheme is independent of the TCP variant used in the network. Extensive simulation results show that the two mechanisms exhibit complementary behavior in achieving the desired differentiation throughout the traffic load space: the TCP-PEP agents control differentiation at low system utilization, whereas the MAC scheduler becomes the dominant differentiation factor at high load.