BasedontheSSTandwavedataobservedbyvesselspassingthroughtheNanshaIslandswaters,thispaperanalysesElNinoevent’seffectonhydrologicalfactorsintheabovewaters.Thepaperconcludes(1)SSTintheNanshaIslandswatervarieswiththatoftheEasternEquatorialPacificOceaninsynchronousphase,butvarieswiththatoftheWesternEquatorialPacificOceaninoppositephase;(2)theseastateinNanshaIslandswatersisrough,thefrequencyofgreatwaveincreasesintheyearofElNino,especiallyinthenextyearoftheyearofElNino.Thepaperdiscussesthereasonsfortheabovephenomena.