Abstract. This aim of this paper is to assess the use of the heterotrophic/autotrophic ratio as an early indicator of trophic status as a part of development of a real time monitoring program at Anjos Bay, Rio de Janeiro, Brazil. An in-situ flow cytometer was used to quantify the abundances of phytoplankton and cyanobacteria, which were identified by chlorophyll and phycoerythrin autofluorescence, respectively. Heterotrophic prokaryotes and viruses were quantified by DNA-binding fluorochromes; merozooplankton larvae were collected by plankton net and quantified by stereomicroscopy. The temporal and spatial distributions of these variables were evaluated on the basis of weekly observations from August 2006 to September 2007. The heterotrophic/autotrophic ratio and the viral abundance were correlated with upwelling events and assume an apparently seasonal pattern. A possible control mechanism and influential factors are discussed, and it is concluded that this ecosystem is bottom-up controlled under eutrophic conditions and top-down controlled under oligotrophic conditions.