This paper focuses on two of the largest rivers and estuaries of Papua New Guinea (PNG), the Fly and Sepik and explores the degree to which river input and estuarine reactions affect the rare earth element (REE) composition of surface sea water in the western Tropical Pacific Ocean. The dissolved phases of the Fly and Sepik River waters have striking REE compositions in the form of large MREE-enrichments as defined by a gradual increase in their shale normalized ratios toward the middle of the REE series. This river/weathering signature is quite distinct from the REE composition of Pacific Ocean sea water. Large scale removal of dissolved river REE occurs in the low salinity regions of the Fly and Sepik River estuaries due to the coagulation of Fe-humic colloids. Laboratory experiments show that the reaction of Fly River particles with sea water leads to the preferential release of MREE to estuarine waters. Additional experiments suggest that the development of MREE-enrichments in PNG rivers is associated with phosphate minerals and their aquatic chemistry.