While the ultimate goal of kernel-level network stacks is to manage individual packets at line rate, the goal of user-level network monitoring applications is instead to match packets with the flow they belong to, and take actions accordingly. With current improvements in Network Interface Cards hardware and network software stacks, traffic monitors and traffic analyzers are fed with multi-Gbps streams of packets – which de facto pushes bottlenecks from kernel-level networking stack up to user-level applications. In this paper, we argue that flow management is a crucial module for any user-application that needs to process traffic at multiple Gbps, and we study the performance impact of different design choices of the flow management module by adopting a trace-driven emulation approach. While our results do not show a single “best” system settings under all circumstances, they highlight several tradeoffs, in terms of, e.g., the kind of structure, its size, and the computational complexity, that may affect system performance in a non-trivial way. We further make our software tools available to the scientific community to promote sharing of best practices.