Estuaries, being the transitional zones between freshwater and marine environments, are important for protecting and rehabilitating the aquatic environments. Sediments from freshwater and marine environments were studied in Jiulong River Estuary (JRE) in different years for rare earth elements (REEs) and some environmentally important metal and metalloid elements (MMEs). The concentration of REEs ranged from 0.11 (Tm) to 296.20 mg kg−1 (Ce), while that of MMEs ranged from 0.40 (Cd) to 86,000 mg kg−1 (Al). The temporal analysis indicated an increase of both REEs and MMEs contaminants from 2012 to 2018. Fractionation of REEs and Ce and Eu anomalies indicated natural weathering, erosion processes and changes in redox chemistry at the sampling sites. Spatial structure analysis showed relatively higher levels of both REEs and MMEs in the freshwater sediments. These variations among the sampling sites indicated different land use and anthropogenic activities. The values of enrichment factor (EF) and geoaccumulation index (Igeo) indicated anthropogenic sources of accumulation, while, ecological risk assessment (Eix) and potential ecological risk index (PERI) indicated potential hazards for biota due to the accumulation of Pb, Zn and As elements.