Seagrasses are marine plants that play important ecological functions in coastal ecosystems. The species Zostera noltei is widely distributed along the European coasts thriving in a variety of environmental conditions. In this study, the phenolic natural products of Z. noltei have been analyzed quantitatively by using UPLC-MS. Plants from the Natural Park of the Bay of Cadiz (Spain) were shown to contain rosmarinic acid (1) and the flavonoids apigenin-7-0- glucoside (2), luteolin-7-sulfate (7), apigenin-7-sulfate (8), diosmetin-7-sulfate (9), and acacetin-7-sulfate (10). The analysis by UPLC-MS of extracts allowed the quantification of all the compounds and evidenced the intraspecific variations in the profile of natural products among plants collected at different dates and locations within the Bay. The flavonoids 2, and 7-10 were present in all the analyzed samples with a total flavonoid content in the range 12.8-72.3 mg/g dry wt, while rosmarinic acid (1) was only present in some samples, reaching up to 19.6 mg/g dry wt. A distinctive feature of plants from the Bay of Cadiz is the common presence of apigenin-7-sulfate (8) as major flavonoid, differing from plants from other regions whose major flavonoid is diosmetin-7-sulfate (9).