Samples collected by two sediment traps located southwest of Crete in the eastern Mediterranean (EMED) [48A (1953 m) and 48B (950 m)] from June 2005 to May 2006 were used to study fluxes of organic carbon, carbonate and coccolithophores in combination with the variations of Sr/Ca ratios in different individually picked coccolith species. Considering the complexity of the EMED, we validate the use of Sr/Ca ratios as productivity proxy and unravel the varied processes which may influence it. We examined the relationship between the seasonal peaks in export fluxes and the Sr/Ca ratio in coccoliths of three upper photic zone coccolithophores species collected in the traps, Calcidiscus leptoporus, Helicosphaera carteri and Emiliania huxleyi. We aimed at testing whether high export fluxes are correlated with high Sr/Ca ratios, suggestive of higher nutrient-stimulated production, or Sr/Ca ratios are unchanged during high export periods, suggestive of increased export efficiency or scavenging. Periods of enhanced trap fluxes in March and June result from surface water blooms recognized in satellite imagery. An additional peak flux was found in January, but this peak represents re-suspended or recycled material in the water column. The amplitude of seasonal variations in the Sr/Ca ratios of the three investigated species is small in both traps. In the shallow trap, a decrease in the Sr/Ca ratio of C. leptoporus occurred synchronously with minimal fluxes. The other two species were not measured for this period. In the deep trap, no such decrease in Sr/Ca was observed during minimal fluxes, in either C. leptoporus or H. carteri, probably due to a long residence of coccoliths in the water column, recycling and low export efficiency. Absolute Sr/Ca ratios for all species are lower than in other more productive environments like the Bay of Bengal, Arabian Sea, or Sargasso Sea. We conclude that Sr/Ca ratios in coccoliths of surface sediments in the EMED reflect mainly spring-summer bloom conditions averaged over hundreds to thousands of years. In addition, the origin of varying calcite thickness in H. carteri was investigated. The similarity of average Sr/Ca ratios in differently-calcified specimens confirms that coccolith thickness variations in this species result from primary biomineralization processes and not from variable overgrowth by (low Sr) abiogenic calcite in the water column or the sediments. © 2009 Elsevier B.V. All rights reserved.