Hi Tom,
I attach here an image that shows a large part of the the full orbit product (left). You are working on a subset of this full product, New Zealand (right?), indicated by the red circle. On the right is an enlargement of that portion of the image. I show always the TOA RGB, and next to it the medium and high sun glint flags overlaid (taken from the MERIS Level 2 product). The full orbit shows the sun glint area which extends over a large part from north to south, and covers roughly half of the swath where it is at maximum, north of New Zealand. The east coast of New Zealand is still in the high sun glint are, with only some parts in medium glint.
The MCI algorithm works at the top-of-atmosphere signal, i.e. no correction for atmospheric effect and no correction of the sun reflection at the water surface (i.e. sun glint) is performed. The idea of the MCI is to be robust to the atmosphere signal. However, I don't think that there is yet an investigation on the robustness to sun glint. As first approximation sun glint is spectrally flat and an additive term to the water leaving reflectance, but of course transmitted through the atmosphere which has a strong spectral dependence. In any case, I think one should not use the MCI in high glint conditions (and better not using it in even medium glint) until a sensitivity analysis has been done to understand the relationship between sun glint and MCI.
Atmospheric correction algorithms remove the effects of the atmosphere as well as the specular reflection at the water surface (glint). The standard MERIS Level 2 product is able to cope with medium glint but not under high glint conditions. The C2R can work under much stronger glint conditions. That is the reason why apparently you get a reasonable Chl estimate from C2R (at least in some areas in the image, I haven't studied it).
Despite of the above, your observation makes sense that the MCI reveals more meaningful values when shifting the peak and baseline wavelengths a bit more to shorter wavelengths at the (rather low) Chl concentrations you found. The spectral location of the chlorophyll peak depends on the level of chlorophyll concentration, and it is shifting to higher wavelengths with increasing chlorophyll concentration. This red peak is actually a combined effect of the chl spectral absorption at 670nm, the chlorophyll fluorescence and pure water absorption. All these are spectrally fixed, but have different relative importance depending on the chlorophyll concentration and hence it seems as if the peak is spectrally shifting.
Carsten
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