The Process-6 cruise, of the Arabian Sea Expedition of the Joint Global Ocean Flux Study, occurred during an intermonsoon, in October-November 1995. A variety of water column conditions were sampled in terms of euphotic zone depths, autotrophic biomass, resident phytoplankton populations, and nutrients. We use measurements of the rate of primary production, quantities of chlorophyll a, the properties of phytoplankton absorption, daily time course of submarine PAR, and estimates of quantum yield to examine the variability seen. Both phytoplankton absorption and variations in quantum yields contribute to variations in primary production. Offshore populations exhibit a reduction in the apparent maximum quantum yield. ©2005 Copyright SPIE - The International Society for Optical Engineering.