Abstract. Abstract Aim We aimed at investigating changes in major groups of plankton (bacterioplankton, phytoplankton and zooplankton) and bacterioplankton metabolism along a transect covering a littoral, macrophyte dominated zone to a pelagic, phytoplankton dominated zone in the large subtropical shallow lake Mangueira, Rio Grande do Sul State, Brazil. Methods The 3.2 km littoral-pelagic transect (7 points) was sampled in October 2007 in the southern section of the lake. Major taxonomic groups of phytoplankton and zooplankton were counted and identified by optic microscopy. The bacterioplankton was identified by FISH (Fluorescent in situ Hybridization), and bacterial abundance, biovolume and biomass were quantified by epifluorescence microscopy. Primary and bacterial productions were measured by incorporation of radioactive bicarbonate and leucine, respectively. Bacterial respiration was measured by experiments of oxygen consumption, and an extensive data set of limnological variables were measured through standard methods. Results Sharp changes in chemical/physical variables, as well as in bacterial density, biovolume, biomass and bacterial growth efficiency occurred on average at 30% of macrophyte coverage, with most of them increasing towards pelagic zones. The composition of major groups of zooplankton, phytoplankton, bacterial morphotypes and phylotypes indicated that different planktonic assemblies live apart in these two zones. Conclusions Our results demonstrate that macrophytes are a structuring driver of the plankton community and bacterial metabolism in this large subtropical shallow lake.