Tropical oligotrophic coral reef lagoons are areas of high biodiversity. Chlorophyll concentration, a proxy for phytoplankton biomass and primary production, is useful to monitor the carbon balance in the context of the climate change and to validate simulations by coupled biogeochemical models. Chlorophyll monitoring by Aqua/MODIS is examined on the large tropical oligo- to mesotrophic lagoon of New Caledonia (23,900 km2). The classical OC3 algorithm developed for MODIS can only be applied in deep waters. In shallow water, when the water is clear with a weak attenuation, the bottom reflectance influences the surface reflectance and then induces an error in the chlorophyll determination. Here, a new OC3-type polynom, relating satellite reflectance ratios and chlorophyll, was determined from bio-optical data collected during a cruise (Valhybio) on the R/V Alis in the frame of the Programme National de Télédétection Spatiale. From the 22th of March to the 9th of April, data were collected during two surveys of the same network. A total of 170 in situ bio-optical measurements in the South Western and South lagoons of New Caledonia were obtained, within a 2 weeks interval (70 non-cloudy match-ups). Four Modis images were acquired during this cruise with moderate to good atmospheric conditions. The new polynom gives a RMS of 14.8% and a MNB of - 9% and gives a better representation of the "true" water column chlorophyll concentration of the New Caledonia lagoon.© (2008) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.