Several methods to monitor cyanobacteria exist, based partly on characteristics that differentiate cyanobacteria from other phytoplankton, such as pigmentation and morphology. However, it is not certain whether all methods give similar insights into the development and properties of a cyanobacterial bloom. It is important to understand the level of consistency of measurements, especially in the case of novel methods. In situ imaging flow cytometry provides community composition information at high frequency but has been little used for filamentous bloom-forming cyanobacteria. To understand if different methods agree, we compared multi-year biomass data collected with Imaging FlowCytobot (IFCB), CytoSense (CS), phycocyanin (PC) and chlorophyll (Chl) a fluorescence, and turbidity sensors, light microscopy, and satellite-based Frequency of Cyanobacteria Accumulations (FCA). Continuous high-throughput data was recorded at Utö Atmospheric and Marine Research Station in the Baltic Sea during summers 2018-2022, along with samples for light microscopy and adjacent satellite observations. The IFCB cyanobacteria biomass pattern most closely resembled those of CS and PC fluorescence. IFCB also described the blooms similarly to FCA, and to some extent to turbidity, but differed from Chl a fluorescence. IFCB and light microscopy agreed on the bloom development and species composition but differed concerning exact biomass. Our study demonstrates that both IFCB and CS are suitable for studying filamentous cyanobacteria and that in situ imaging flow cytometry provides valuable support for cyanobacteria monitoring by yielding detailed high-frequency taxon-specific information. Still, the best overall coverage of rapid biological processes such as bloom development is achieved with the parallel use of multiple observation techniques.