In the present work, we assessed the contents of rare earth elements (REEs), including yttrium and scandium, in rhizomes and leaves of the widespread seagrass Zostera noltei Hornemann 1832 and in the nearby sediments from the Black Sea coast. The total REE content in the sediments was found to be much higher than in Z. noltei. The order of decrease in the major REE contents in the sediments and the seagrass rhizomes was identical, except for La and Y. La was the most abundant in the sediments, and Y in the rhizomes. The contents of all REEs in rhizomes of Z. noltei were 1.5–10 times higher than in the leaves. The highest difference in the REE contents was found for the minor elements (Sm–Lu). The translocation factors for Sc and the minor elements (excluding Tb) from the sediments to the rhizomes and from the rhizomes to the leaves turned out to be pairwise equal, which indicates the similarity of the REE translocation mechanisms. Comparing our results with the literature data, it is possible to conclude that the seagrass Z. noltei does not have an advantage in the REE accumulation over marine macroalgae. At the same time, large coastal deposits of this seagrass after storms allow us to consider it as a possible source of REEs in the future.