As most port areas throughout the world, Guanabara Bay (GB), which hosts the Harbour of Rio de Janeiro (HRJ), is under intense environmental stress. Located in one of the most iconic places of the world, GB environmental status has been the focus of worldwide attention with the imminent 2016 Olympic Games. The aim of this study was to discuss all past and current relevant aspects to characterize the environment of GB and its main harbour, including geomorphology, climatology, hydrology, geography and biodiversity aspects. A historical view of the social and economic setting, as well as the major threats to the bay environment such as increased pollution, sedimentation, marine debris, cultural eutrophication, bioinvasions, resource utilization, climate change and habitat loss discussed. Aiming to identify – and possibly manage – the threats to biodiversity in harbour areas, a case study comparing the HRJ with the nearby Arraial do Cabo harbour was included. At last, conclusions were drawn so as to highlight effective measures to reduce the environmental degradation of the bay and the harbour.