We measured water leaving reflectance, phytoplankton pigments, optical properties and photosynthetic parameters in the southern Benguela ecosystem in October 2002. These data were used to validate MERIS standard products: reflectance (MERIS wavelengths) and Case 1 Chlorophyll‐a. In this heterogeneous area, accurate validation required sampling within a few minutes of the satellite overpass. Inter‐pigment relationships e.g. Total Chlorophyll (TChla) to Total Pigment (TP) were robust (R²∼0.99) yet pigment ratios (TChla/TP) were not constant (range 0.44 to 0.62) increasing log‐linearly with biomass (R²∼0.7). Photosynthetic parameters (e.g. Photosynthetic Quantum Efficiency, PQE) and optical ratios (a₆₇₆/a₄₄₀) also increased log‐linearly with biomass (R²∼0.8). PQE, pigment and optical ratios were linearly inter‐correlated (R²∼0.7 to 0.8). From these data we derived the bio‐optical traits for several phytoplankton functional types (PFTs): micro‐plankton (diatoms and dinoflagellates) had high biomass, pigment ratios and PQE; nano‐flagellates had low to intermediate biomass, pigment ratios and PQE; prokaryotes had very low biomass, pigment ratios and PQE. We present MERIS data analysed for PFTs and new products (PQE).