Just as confusing as it can be to see a noun that has two different forms of the plural, we also sometimes come across nouns that appear to have two different genders. Whether we talk about “der See” or “die See” depends on the context and meaning.
“Der See” simply means “the lake”.
“Die See” means “the sea, the ocean”. Other popular words with a similar meaning are “das Meer” or “der Ozean”.
The plural for both of these forms is “die Seen”. The meaning of the plural is context driven, i.e. you cannot just by looking at the word determine whether we talk about “lakes” or “oceans”, however, it is much more common in German to speak of “die Seen” when talking about “the lakes” and instead to substitute “die Meere” when speaking about “the oceans” in the plural.
The best way to memorise these distinctions is probably by simply memorising the name and gender of one proper lake and of one proper ocean. Once you have done that you should never have problems again with the meaning or grammatical gender of these words, e.g.:
der Bodensee (Lake Constanze)
die Ostsee (the Baltic Sea)