The objective is to describe and quantify the diel variability of water quality in a tropical coastal system, Guanabara Bay, Brazil. Water samples were collected in spring and neap tide cycles over 24 h periods at three strategic sites. A pollution gradient was evident between the sampling sites. The average fecal coliform values decreased from 106 (site 3, most polluted) to 101 (site 1, less polluted). Organic matter mineralization was found in a similar gradient to organic pollution. However, complete nitrification was only found associated to regions where the water quality was better. Variability in this data set was determined mostly by the pollution gradient observed, and by tidal influence as well. The poor water quality indicates that the bay undergoes severe environmental stress. However water renewal promoted by tidal action was an important mechanism in diluting the pollution, improving water quality even in ebb tides and in the inner channels. The significance of micro-scale changes in water quality assessment in Guanabara Bay was confirmed, as well as the importance of these strategic sampling sites, reinforcing the importance of these measurements in monitoring programs.