Dissolved nutrients, phytoplankton biomass and other ancillary variables, were obtained at two sub-embayments at the entrance of Guanabara Bay (Rio de Janeiro, Brazil) and a composite trophic status index (TRIX) was used to assess the water quality of the study area. The role of bottom sediments in nutrient dynamics was also investigated through the evaluation nutrients, phytoplankton biomass and other sedimentary variables, since this compartment acts as a geological record of anthropogenic input. Jurujuba Sound, at the east margin, and Flamengo-Botafogo Sounds, at the western margin, were sampled during neap and spring tides in the dry season. Signs of eutrophication were detected through the extreme variations of dissolved oxygen concentrations at both margins, being more accentuated at Jurujuba Sound (2.20-14.07 mg.l-1). Dissolved inorganic nitrogen was elevated at both margins and mostly composed of ammonium, surpassing 87% at Flamengo Botafogo Sounds, which suggests a continued input of raw sewage at the western margin of the bay. TRIX revealed poor water quality for most stations at the study area, varying from 4.53 to 7.29 at Jurujuba Sound and from 5.67 to 7.87 at Flamengo-Botafogo Sounds. The increase of TRIX from neap to spring tide was registered at both margins, revealing decrease of water quality. The differences in grain size between both margins played a key role in nutrient dynamics, with predominance of fine sediments at Jurujuba Sound and coarser particles at the opposite margin. Accumulation of high concentrations of TOC (0.87-6.57%) and inorganic phosphorus (154.34-1516.82 µg.g-1) were favored by the predominance of fine sediments at Jurujuba Sound. The assessment of eutrophication in water column and bottom sediments revealed the maintenance of this process at the entrance of Guanabara Bay sustained by the recurrent anthropogenic input, what demands urgent action from public policies to mitigate this situation.