Spatio-temporal variations of chlorophylls and phycoerythrins, inferred by spectrofluorometric methods, were studied from April 2002 to June 2003 in the southwest lagoon and oceanic waters of New Caledonia. Trade winds blew 75% of the time and appeared as the main factor influencing surface Tchl (sum of monovinyl- and divinyl-chlorophyll ) variations in the ocean, near the barrier reef. Lagoon and oceanic waters differed in the composition of picoplanktonic cyanobacteria with a relative dominance of Prochlorococcus and high-phycourobilin Synechococcus in the ocean, and a relative dominance of high-phycoerythrobilin Synechococcus in the lagoon. Main pigment variations in the lagoon were associated with cyclone Erica in March 2003 and showed a 5-6 fold Tchl increase around Nouméa. The cyclone stimulated mainly diatom growth as indicated by the high chlorophyll ( )/chlorophyll ratio and by the lowest values for the other pigment ratios. The relative importance of divinyl-chlorophyll concentration and fluorescence excitation spectra of phycoerythrins appeared as useful tools for characterizing lagoon-ocean exchanges.