Growth of submerged and emergent macrophytes was studied together with heterotrophic bacterioplankton abundance and production in two Hungarian shallow lakes with dominant macrophyte covers. It was expected that bacterioplankton numbers and activity would have an effect on macrophyte biomass accumulation. Bacterial production and abundance showed a strong seasonal pattern with maximum in the warmest months (July, August). It was found that macrophyte biomass increased with heterotrophic bacterial production and abundance up to 5.6 µg C l− 1 h− 1 and 5.30*106 cells, respectively, while over that value was negatively associated with macrophyte growth. It was also shown that the relationship between heterotrophic bacteria and macrophytes also varied seasonally, showing a multifaceted relationship. It was demonstrated that macrophytes are not only the most significant carbon and energy source for the bacteria in shallow, macrophyte-dominated lakes, but are also competing organisms that could be supressed by excessive bacterial activity. These findings could help better understand the interaction between macrophytes and bacterioplankton, and assist wetland managers in quantifying what may be a primary cause of reed die-back.