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Abstract: Submerged macrophyte vegetation has been mapped in four calcareous groundwater-fed streams in Bavaria (southern Germany) in order to compare and assess two different methods of river bioindication. The first one, the trophic index of macrophytes (TIM), is a tool to assess the trophic status of running waters. In contrast, the reference index (RI) is an ecological index which evaluates the difference between a reference community and the actual submerged vegetation, depending on the river type, as required by the Water Framework Directive. Water nutrient concentrations were measured once at selected sites in all water courses. The TIM reflects water phosphorus concentrations, accounting also for nutrients enrichment in the sediment, and is not influenced by shading, depth, substrate and flow velocity of the water course. The TIM is very sensitive to small variations in P concentration when the P level is low, while the index tends to a maximum as soluble reactive phosphorus (SRP) and total phosphorus (Ptot) exceed a certain value. The RI indicates river ecological status which is not only influenced by trophic status but by every factor leading to a deviation of the actual macrophyte community from the reference community. In the investigated rivers the RI indicated reduced flow velocity caused by milldams and shading by riparian vegetation, in addition to trophic status. In rivers that are at the boundary between two different river types, classification of river type can play a crucial role for river status assessment. Incorrect classification of river type can lead to both, a “too good” and “too bad” assessment. [Copyright &y& Elsevier]