Seasonal and interannual variations of the New Guinea Coastal Current (NGCC) and New Guinea Coastal Undercurrent (NGCUC) were investigated by examining the 5 years' data from acoustic Doppler current profiler moorings at two sites (2°S 142°E, 2.5°S 142°E) off the New Guinea coast. The NGCC flowed northwestward as is usual and intensified during the boreal summer, then weakened or even reversed direction to southeastward during the boreal winter. This seasonal change correlated to the monsoonal wind variation. However, during the 1997–1998 El Niño, the southeastward NGCC during the boreal winter was not observed, and northwestward flow was dominant throughout the year. On the other hand, the NGCUC flowed steadily northwestward all year-round and intensified during the boreal summer. During the growing phase of the El Niño, the NGCUC intensified, and its northwestward flow reached from the surface to a depth of 250 m. Comparison between the volume transport of these currents and the Sverdrup transport along 2°S in the ocean interior indicated a mean difference of 13 × 106 m3 s−1 northward. The relationship between variations of these two transports showed a negative correlation on seasonal timescales except during the El Niño. During the mature phase of the El Niño, northward Sverdrup transport was enhanced significantly, furthermore the transport of these currents was also northward. The result demonstrates a process by which anomalous water volumes can flow into the equatorial region due to an imbalance between the volume transport in the ocean interior and the western boundary.