Kasper if you find it in the field, you can identify it by its location. Z. marina is almost always subtidal requiring full submergence, while Z. noltii is intertidal since it needs to be exposed periodically to air.
Additionally Z. marina has a maximum leaf length of about 1 m, but typically between 20 - 50 cm. Z. nolti by the other hand is smaller and has a maximum length of around 22 cm. The leaf width of Z. nolti is also smaller (0.5 - 1.5 mm). In Z. marina you can have leaf widths of about 4 - 10 mm wide. If you have flooring shoots is even easier to distinguish. The flooring shoots of Z. noltii are un-branched or with a few branches near the base. In Z. marine they are very branched.
The easiest way to distinguish between the two species is to look at the apex of their leaves (blades). In Z. marina the apex of the blade is rounded to mucronate, while in Z. notlii the blade apex is often emarginated and asymmetric.
Kuo and den Hartog provide an excellent chapter on seagrass taxonomy and identification, please check this link: