Structural health monitoring (SHM) is increasingly used in civil engineering. One of its main purposes is to detect and assess changes in infrastructure conditions to reduce possible maintenance downtime and increase safety. Ideally, this process should be automated and implemented in real time. Recent advances in sensor technology facilitate data collection and process automation, resulting in massive data streams. Functional data analysis (FDA) can be used to model and aggregate the data obtained transparently and interpretably. In two real-world case studies of bridges in Germany and Belgium, this paper demonstrates how a function-on-function regression approach, combined with profile monitoring, can be applied to SHM data to adjust sensor/system outputs for environmental-induced variation and detect changes in construction. Specifically, we consider the R package funcharts and discuss some challenges when using this software on real-world SHM data. For instance, we show that pre-smoothing of the data can improve and extend its usability.