Heterogeneous communication networks with their variety of application demands, uncertain time-varying trafc load, and mixture of wired and wireless links pose several challenging problem in modeling and control. In this paper we focus on the round-trip time (RTT), which is a particularly important variable for efficient end-to-end congestion control. Based on a simple aggregated model of the network, an algorithm combining a Kalman lter and a change detection algorithm is proposed for RTT estimation. It is illustrated on real data that this algorithm provides estimates of significantly better accuracy as compared to the RTT estimator currently used in TCP.We also analyze how wireless links affect the RTT distribution. Link re-transmissions induce delays which do not conform to the assumptions on which the transport protocol is based. This causes undesired TCP control actions which reduce throughput. A link layer solution based on adding carefully selected delays to certain packets is proposed to counteract this problem.