Water mass characteristics in the waters around Maluku are influenced by the water mass of the Pacific Oceans. The parameters used to see the changes when the El Nino and La Nina are the sea surface temperature, salinity and TS diagram patterns. Generally, this research aims to examine the relationship of the Pacific Ocean and the Banda Sea in 1993 to 2000 (normal condition, El Nino and La Nina events) to the climate conditions in the Maluku. The study was conducted using the data CTD World Ocean Database and climate data from the European Center for Medium-Range Weather Forecasts in the waters around Maluku. There are two types of water masses Affect the Banda Sea, which is can be seen from the two types of density, each of σt = 26.0 kg/m3 with a salinity maximum 34.9 psu at a depth of 230 m, shows the influence of the water Mass of the South Pacific. The density of σt = 23.7 kg/m3 with a maximum salinity of 34.83 psu at a depth of 127 m, shows the influence of the water mass of the North Pacific. The relationship between the water mass and the climate are clearly shown during the 1998 El Niño, surface salinity value (33.8 psu) higher than normal conditions (33.65 psu). The SST Indices value in 1998 indicates a significant anomaly with values ranging from + 3.2 to - 1.2. The pattern of sea surface temperature anomaly change is inversely proportional to the pattern of rainfall, where when the anomalous value of sea surface temperature increases then the value of rainfall will be reduced. Meanwhile, during the La Nina at 1999-2000 average value of surface salinity (34.3 psu), are higher than normal conditions (34.56 psu) which means during The El Nino and La Nina changes the water mass and climate around the Maluku.