Large-scale stream processing systems often follow the dataflow paradigm, which enforces a program structure that exposes a high degree of parallelism. The Timely Dataflow distributed system supports expressive cyclic dataflows for which it offers low-latency data- and pipeline-parallel stream processing. To achieve high expressiveness and performance, Timely Dataflow uses an intricate distributed protocol for tracking the computation’s progress. We modeled the progress tracking protocol as a combination of two independent transition systems in the Isabelle/HOL proof assistant. We specified and verified the safety of the two components and of the combined protocol. To this end, we identified abstract assumptions on dataflow programs that are sufficient for safety and were not previously formalized.