Freshwater classification according to the Water Framework Directive (WFD) is based on estimation of the deviation between biological elements found on river stretch in comparison with communities detected in the same river type under reference conditions (undisturbed and near-natural habitats). We present analyses to describe macrophyte development in pristine lowland rivers and to reveal the variation among various stream types. The study is based on a country-wide survey of Poland with a dataset of 642 sites on 367 water courses. Surveyed rivers covered the whole lowland area of Poland. Field surveys were conducted using the Polish macrophyte approach, which enabled calculation of several macrophyte metrics. Firstly, a numerical index MIR (Macrophyte Index for Rivers) was computed, which reflects river degradation, especially eutrophication. Furthermore, five diversity metrics were calculated. Each survey, in addition to macrophyte assessment, was supplemented by a complex suite of environmental records. Reference conditions were defined using four criteria: (1) catchment land use, (2) hydromorphological features, (3) water quality and (4) biological assessment. The selected reference lowland rivers included 40 sites. To classify plant data, two-way indicator species analysis Twinspan was used. This resulted in distinguishing four endclusters which were heterogeneous according to plant composition: organic rivers and three types of siliceous rivers (small with sandy substrate, small with stony substrate and large rivers). The differentiation of environmental factors between river types was confirmed by a variance analysis (ANOVA). Furthermore, the environmental database was explored with principal component analysis (PCA). The PCA principal components were analysed against river types with the canonical correspondence analysis (CCA). Finally botanical differences between identified river types have been detected, using botanical metrics the share of different macrophyte groups and relationships with particular species were defined.