The Sundarbans, the world's largest mangrove forest, confronts potential threats from various anthropogenic activities leading to degradation of its aquatic ecosystem. To examine the current status of the aquatic ecosystem, this study aimed to evaluate the spatial and seasonal fluctuation of three principal water quality attributes namely Chlorophyll-a (Chl-a), Total Suspended Matter (TSM), and Colored Dissolved Organic Matter (CDOM) in the complex tidal river systems of the Sundarban mangroves forest using earth observation and in-situ data. A set of two bio-optical algorithms, Ocean color-2 (OC-2) and Ocean color-3 (OC-3), were applied to measure Chl-a concentration, Green/NIR and the Red/NIR band ratio algorithms were used for TSM and the Case-2 Regional Coast Color (C2RCC) processor in the SNAP software was applied to obtain CDOM concentration in study area. A total of 50 in-situ samples were collected during post-monsoon and pre-monsoon to validate the results. Our results clearly demonstrated seasonal variability with higher Chl-a concentrations in post-monsoon than pre-monsoon. This was due to the OC-2 algorithm which produced better results with R2 = 0.73, RMSE = 0.27 for post-monsoon and R2 = 0.55, RMSE = 0.32 for pre-monsoon. Whilst, TSM concentration performed the best with R2 = 0.77; RMSE = 15.82 and R2 = 0.65; RMSE = 33.96 in post-monsoon and pre-monsoon according to the Green/NIR band ratio method. The nearshore and narrow waterway regions had the highest concentrations of TSM and Chl-a, whereas the offshore regions had the lowest. Strong association were observed between the in-situ and satellite derive absorption coefficient, aCDOM (m−1). The R2 for a CDOM during pre-monsoon was 0.65 and throughout the post-monsoon, it was 0.74. Pre-monsoon concentrations were found to be higher due to marine sources and higher wind speeds, possibly due to sediment resuspension. This kind of baseline evaluation will help to detect threats, direct preventive measures for the protection of biodiversity, and deepen our knowledge of these distinct ecosystems. The results will help develop flexible management and preservation plans that can adjust to both natural and man-made changes.