Interesting. There is no current legislation for the protection of phytoplankton species and zooplankton in United States that I know of. I'm curious to ask why you would like to know?
Because I think that before thinking about protecting marine species, we must think of protecting their food, and the lungs of the oceans, it is very important. Humans have destroyed all the natural sources of oxygen
The Water Framework Directive does not directly protect phytoplankton or zooplankton species as far as I know but assessments of ecological status based on benthic diatom communities should contribute indirectly to protection of phytoplankton species.
Ecologically, it makes sense to preserve the species. Think of phytoplankton like the leaves of grass, leaves on trees, leaves everywhere on the Earth, on land. Such an abundance no? Their reproduction rates vary but a typical turnover rate is 24 hours?
But, there are other phenomena in the ocean especially (marine ecosystems are more complicated and more sensitive than the land area), then it's true, phytoplankton may recur in 24 hours, but the problem that there are species that resist the anthropogenic changes but against other species was only disappear ground, ie species abundance (resistant) to other (sensitive). And since this is a food chain that will disrupt the local and global ecosystem.
All things considered, phytoplankton are microbial species and grow very fast. There is legislation in place to protect the quality of the waters in which we can have plankton grow in protected waters.
I think it is better to protect the water that will eventually protect every organism in it include phytoplankton. There are thousands or even hundred thousands of phytoplankton and zooplankton that are not identified yet and to protect them is necessary in order to preserve the food web in both freshwater and seawater
Wa Iba is right. It would make no sense to protect some species to the detriment of others among the known species (and forget that these probably are only a small percentage of all species present (see e.g. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001127, although predicted species vary widely, depending on the parameters used to get an estimate).
To me, given this situation, the best bet is to put in place (as is being done) legislation to protect their environment, and leave the laws of nature to do their job, saving or eliminating species as needed to preserve a functional ecosystem