variations of nanoplankton (2-20 μm) and filamentous bacteria (diameter: 0.5-2.0 μm) of guanabara bay (rj, brazil) are presented, considering cell density and carbon content of auto- and heterotrophs. our goal is to contribute to future modeling of local trophic dynamics. subsurface water samples were taken weekly during the year 2000 at two sites: urca (close to the entrance, more saline, eutrophic) and ramos (inner area, less saline, hypertrophic). microscopic analysis was done by epifluorescence and cell density was converted to biomass through cell biovolume. total nanoplankton was about 108 cells.l-1 in most samples (>57%), and total filamentous bacteria densities varied from 105 to 108 fil.l-1. autotroph density was one order of magnitude higher at ramos, both for nanoplankton (md: 108cells.l-1 at ramos and 107cells.l-1 at urca) and for filamentous bacteria (md: 106 fil.l-1 at ramos and 105 fil.l-1 at urca). the same was observed for autotrophic biomass (md: 103μgc.l-1 at ramos and 101μgc.l-1 at urca for nanoplankton; md: 28μgc.l-1 at ramos and 1.4μgc.l-1 at urca for filamentous bacteria). the relative contribution of autotrophs increased after conversion to biomass. seasonal variation was conspicuous for filamentous bacteria at both sites and for nanoplankton only at ramos, with maximum autotrophic abundances during the rainy period (spring-summer).