Asia's largest brackish water ecosystem, Chilika lagoon, supports livelihood of millions of inhabitants and also known to be bio-geo-chemically dynamic. This demands continuous monitoring of lagoon for which optical remote sensing may be crucial. The in situ bio-optical parameters were analyzed in two sectors (Outer Channel: OC and Southern Sector: SS) of Asia's largest brackish water ecosystem, Chilika lagoon. The spectral Remote Sensing Reflectance (Rrs) ranged from 0.003 to 0.02sr-1 in OC whereas in SS it was between 0.003 and 0.028sr-1. The minimum Rrs was at 400nm that gradually increased with a peak at 580nm and subsequently decreased towards longer wavelength. Rrs exhibited similar pattern in both the sectors from 400 to 600nm. Beyond this wavelength, Rrs was relatively higher in SS. The shifting of peak towards longer wavelength could be attributed to high absorption due to chlorophyll-a (chl-a) and chromophoric dissolved organic matter (CDOM) that varied largely between sectors with relatively higher concentration of chl-a in OC and CDOM in SS. Further, we modelled chl-a by seven ocean colour algorithms (OC4, OC4E, OC4O, OC3M, OC3V, OC3C and OCMO2) using in situ Rrs. The modelled chl-a was overestimating in situ at all stations due to high concentration of CDOM contaminating chl-a signals. However in OC, in situ and modelled chl-a followed the same trend (R2=0.88 to 0.90) probably due to strong co-variance of chl-a with CDOM. The analysis of this study points out towards the requirement for sector specific bio-optical algorithm for accurate chl-a retrieval for synoptic monitoring of lagoon health.