The European Water Framework Directive has required chemical and biological assessments in waterbodies. While studies of water chemistry uncertainties have existed for a long time, few studies have been carried out in hydrobiology. Our aim was to study the role of uncertainties defined as any action that may cause a data error on the French index “Indice Biologique des Macrophytes de Rivières” IBMR based on the macrophyte compartment. IBMR gives the trophic status of the river. The selected uncertainties were based on the surveyor effect both in situ and in laboratory, such as taxa omission, species identification error and cover class error. We proposed an innovative approach close to sensitivity analysis using controlled virtual changes in taxa identification and cover classes based on two confusion matrices. The creation of new experimental floristic lists and the calculation of metrics according to random specified errors allowed us to measure the effect of these errors on the IBMR and the trophic status. The taxa identification errors and combined errors (taxa identification and cover class) always had a stronger impact than cover class errors. To limit their impact, surveyor training, confrontation between surveyors and a quality control approach could be applied.