Many toxic and/or noxious cyanobacteria appear in nature with a filamentous, stacked cell arrangement called trichomes. Although water treatment can be optimized to keep cyanobacterial cells intact and to avoid the release of toxic and/or noxious compounds, many physical and chemical stresses encountered during the treatment process may result in trichome truncation, decreasing treatment efficiency by allowing single cells or short trichomes to reach the product water. This makes it possible for harmful/noxious compounds as well as organic matter to enter the distribution system. Investigations in a pilot and three full-scale water treatment plants were carried out in order to elucidate the degree of trichome truncation across different unit processes. It was found that genera (Pseudanabaena, Planktolyngbya) with short trichomes ( < 10–12 cells per trichome), are hardly affected by the unit processes (loss of one to four cells respectively), while genera (Planktothrix, Geitlerinema, Dolichospermum) with longer trichomes (30+ cells per trichome) suffer from high degrees of truncation (up to 63, 30, and 56 cells per trichome respectively). The presence of a rigid sheath and/or mucilaginous layer appears to offer some protection from truncation. It was observed that certain unit processes alter the sensitivity or resilience of trichomes to disruption by physical stress. Some genera (Planktothrix, Geitlerinema) were sensitive to pre-oxidation, making them more susceptible to shear stress, while Dolichospermum sp. appears more robust after pre-oxidation. While the potential of toxicogenic genera breaking through into the product water is a real danger, in the current study no toxicogenic cyanobacteria were observed. This work stresses the need for plant operators to study the incoming cyanobacterial composition in the raw water in order to adjust treatment parameters and thus limit the potential of toxic/noxious compound breakthrough.