In manufacturing industry, downtimes have been considered as major impact factors of production performance. However, the real impacts of downtime events and relationships between downtimes and system performance and bottlenecks are not as trivial as it appears. To improve the system performance in real-time and to properly allocate limited resources/efforts to different stations, it is necessary to quantify the impact of each station downtime event on the production throughput of the whole transfer line. A complete characterization of the impact requires a careful investigation of the transients of the line dynamics disturbed by the downtime event. We study in this paper the impact of downtime events on the performance of inhomogeneous serial transfer lines. Our mathematical analysis suggests that the impact of any isolated downtime event is only apparent in the relatively long run when the duration exceeds a certain threshold called opportunity window. We also study the bottleneck phenomenon and its relationship with downtimes and opportunity window. The results are applicable to real-time production control, opportunistic maintenance scheduling, personnel staffing, and downtime cost estimation.