With the advent of high speed links, online flow measurement for, e.g., flow round trip time (RTT), has become difficult due to the enormous demands placed on computational resources. Most existing measurement methods are designed to count the numbers of flows or sizes of flows, but we address the flow RTT measurement, which is an important QoS metric for network management and cannot be measured with existing measurement methods. We first adapt a standard Bloom Filter (BF) for the flow RTT distribution estimation. However, due to the existence of multipath routing and Syn flooding attacks, the standard BF does not perform well. We further design the double-deletion bloom filter (DDBF) scheme, which alleviates potential hash collisions of the standard BF by explicitly deleting used records and implicitly deleting out-of-date records. Because of these double deletion operations, the DDBF accurately estimates the RTT distribution of TCP flows with limited memory space, even with the appearance of multipath routing and Syn flooding attacks. Theoretical analysis indicates that the DDBF scheme achieves a higher accuracy with a constant and smaller amount of memory compared with the standard BF. In addition, we validate our scheme using real traces and demonstrate significant memory-savings without degrading accuracy.