The species diversity of macrophytes and their abundance in middle-sized streams of Latvia were investigated. On the basis of environmental factors (stream width, water depth, substrate type, shading, and flow velocity), five major groups of streams were distinguished representing mutually exclusive macrophyte communities—(1) fast flowing streams on gravel substrates, (2) slow flowing streams on gravel substrates, (3) fast flowing streams on sandy substrates, (4) slow flowing streams on sandy substrates, and (5) streams with soft, silty substrates. A total of 48 macrophyte taxa were found in 72 surveyed sites. The most frequent species in the investigated streams were Sparganium emersum, S. erectum s.l., Nuphar lutea, Veronica beccabunga, as well as the invasive alien Elodea canadensis. The species richness ranged from 2 to 22 per site, and Shannon diversity index varied from 0.61 to 2.88. The highest species richness (22) was found in slow flowing streams with gravel substrates. Poor macrophyte composition was characteristic for fast flowing streams on sandy substrates.