The in-field protein production of four macroalgae (Gracilariopsis vermiculophylla, Gracilaria gracilis, Gracilariopsis longissima, Ulva australis) and three seagrasses (Cymodocea nodosa, Zostera marina, Zostera noltei) was investigated in four transitional water systems over one year. The protein content in macroalgae ranged from 1.0 to 25.1% and was inversely related with water temperature. The annual protein production was the highest for G. longissima (500 g dw m−2 year−1), followed by G. vermiculophylla (350 g dw m−2 year−1), U. australis (33 g dw m−2 year−1) and G. gracilis (270 g dw m−2 year−1). The most productive months spanned between March and August for G. longissima and between December and May for G. vermiculophylla, reaching 78% and 85% of the annual production, respectively. The protein production was more uniform over the year for the other two macroalgae. The protein production in seagrasses was averagely from 3.4 to 12 times lower than in macroalgae and reached 77.8 g m−2 year−1 in C. nodosa, followed by Z. marina with 55.6 g m−2 year−1 and Z. noltei with 30.6 g m−2 year−1. The peak production between April and August accounted for 63–98% of the annual production. Rhizomes displayed the lowest protein contents (1.2–3.4%), almost half in comparison with leaves (2.3–5.1%) and the lowest protein production with 21.0 g m−2 year−1 for C. nodosa, 6.3 g m−2 year−1 for Z. marina and 9.0 g m−2 year−1 for Z. noltei. Aquatic macrophyte productions proved to be competitive with the main crops currently cultivated on land without competing in terms of land and freshwater destination. The challenge is still open on the front of digestibility and protein extraction but sustainable management and production of macrophytes (especially macroalgae) can significantly contribute to the global protein production in coastal areas.