The Guanabara Bay (GB) is an estuarine system in the metropolitan region of Rio de Janeiro (Brazil), with a surface area of $∼346km2$ threatened by anthropogenic pressure. Remote sensing can provide frequent data for studies and monitoring of water quality parameters, such as $chlorophyll-a$ concentration ($Chl-a$). Different combination of Medium Resolution Imaging Spectrometer (MERIS) remote sensing reflectance band ratios were used to estimate $Chl-a$. Standard algorithms such as Ocean Color 3-band, Ocean Color-4 band, fluorescence line height, and maximum chlorophyll index were also tested. The MERIS $Chl-a$ estimates were statistically compared with a dataset of in situ$Chl-a$ (2002 to 2012). Good correlations were obtained with the use of green, red, and near-infrared bands. The best performing algorithm was based on the red (665 nm) and green (560 nm) band ratio, named “RG3” algorithm ($r2=0.71$, $chl-a=62,565*x1.6118$). The RG3 was applied to a time series of MERIS images (2003- to 2012). The GB has a high temporal and spatial variability of $Chl-a$, with highest values found in the wet season (October to March) and in some of the most internal regions of the estuary. Lowest concentrations are found in the central circulation channel due to the flushing of ocean water masses promoted by pumping tide.