MANETs are wireless networks consisting of dynamic nodes that are self-configurable and infrastructure-less. The traditional layered architecture is designed for wired networks, and it runs into performance issues when deployed for Ad-hoc networks. Research focus has shifted towards cross layered architecture to break the traditional layered architecture. This paper proposes a joint optimization of Transport and Network layers by collaborating with physical layer to procure information such as signal power and battery level. To address congestion issue, a mathematical model on window based exponential averaging of received signal powers is suggested at the transport layer, so that TCP can proactively engage in making appropriate decision to address node disconnection problem. To reduce the flooding overhead in routing mechanism, a cross-layered location restricted energy efficient routing approach is suggested to achieve end-to-end guarantee at the transport layer. This approach is proposed as an alternative to AODV/DSR protocols. Also performance comparison of TCP variants in terms of throughput, congestion window and packet delivery ratio (PDR) is simulated under different network scenarios in NS2 and possible reasons for packet loss are identified. © 2014 IEEE.