While rare earth element (REE) concentrations and speciation are often investigated by chemical extractions of bulk soils and sediments to elucidate site specific environmental processes and anthropogenic influences, micro- and nano-scale investigations provide more precise insights into the REE-mineral associations essential for understanding REE mobility in complex natural landscapes. In this study we combine the high resolution microscopic techniques of scanning electron microscopy energy dispersive spectroscopy (SEM-EDS), transmission electron microscopy (TEM) and electron energy-loss spectroscopy (EELS) to characterise micro- and nano-scale REE-mineral associations in an eutrophic estuarine system, specifically at a site containing 1) a coastal acid sulfate soil (CASS) and 2) adjacent estuarine sediments that have received acute acidic drainage from the CASS site for ~20 years. This study revealed particles with a porous morphology that had a reoccurring association between Fe and the REE lanthanum (La:Fe:O = 1:1:3) in the sediments, indicating a presence of either a pure orthoferrite ABO3 compound (A=REE, B=metal), or a co-occurrence of REE and Fe minerals (i.e., La2O3 co-precipitated in 1:1 stoichiometry with Fe oxide). Fe(III) minerals are typical of CASS influenced sites and are likely to be essential REE sinks in this system. Additionally, micro- to nano-scale REE-phosphate particles were also widespread here, which may reflect an important REE sinks in eutrophic sediments. Specifically, a REE-phosphate particle targeted by SEM was thin sectioned by focused ion beam (FIB) for TEM analysis, revealing a crystal structure (a=6.6 Å, b=6.9 Å, α=90°) consistent with monazite ((REEs, Th)PO4). Usually, positive Ce anomaly is more found in oxidised solid phase due to less soluble oxidized Ce(IV)O2. Interestingly, our EELS data revealed that Ce was only present as reduced Ce(III) in our solid sample, showing the possibility of Ce3+ incorporating into less soluble minerals such as REE-phosphate, which may explain the higher positive Ce anomaly observed in insoluble phases in reduced sediment. Microtubular cavities, consistent with abiotic processes in REE-phosphate precipitation, were also observed on the cross-sectioned monazite.