While it is a common trope that the name of the Netherlands is derived from the fact that part of the land lies below sealevel, that is actually not the origin of the name. The etymology of the name goes back well before the widespread use polders, and the meaning is much more mundane than referring to some unique aspect of the Netherlands which the Dutch are proud of.

It is common to divide a river and the surrounding area in an 'upper' and an 'lower' part. To give a couple of examples, there's Upper Egypt and Lower Egypt and there's the Upper Mississippi River and the Lower Mississippi River. In all these cases the 'Upper' part is upstream from the 'Lower' part, and the 'Lower' part is the part between the 'Upper' and the sea.

When the Romans were in the area we're concerned with, they establised several provinces; two of those provinces were Germania Superior (Upper Germania) and Germania Inferior (Lower Germania). Germania Superior coverered the Upper Rhine and tributaries, whereas Germania Inferior covered the estuary of the Rhine, Meuse and Scheldt rivers. So already in the first century A.D. the Romans used a 'Lower' designation for the area which is now Belgium and the Netherlands. This was well before any inpoldering took place.

The Woordenboek der Nederlandse Taal ("Dictionary of the Dutch language") at the entry for "Nederland" gives as a literal meaning "laag gelegen land" ("low-lying country") and says that it was known like that since the Middle Dutch period (1200-1500). They give a 15th century source which mentions the low-lying nature of the country (Middle Dutch "nederigheydt", modern Dutch "Nederigheid": "De hoedanigheid van laag gelegen te zijn; thans verouderd." - "The state of being low-lying; now obsolete.") No mention is made of part of the land lying below sealevel having anything to do with the name.

In short

The Low Countries are called the Low Countries because they lie at the lower part of several rivers and because the land is low-lying, but not because part of the land is (now) below sealevel.

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With that out of the way, let's get down to actually answering your question. In the Late Middle Ages, the name "Low Countries" (and its respective Spanish/Portuguese/Italian/French translations) referred to the area now covered by the Netherlands, Belgium, Luxemburg, and the extreme north of France. These are the 'Seventeen Provinces' which were united by the Burgundians and the Habsburgers. After a revolt the northern provinces formed the "Republiek der Zeven Verenigde Nederlanden" (the "Republic of the Seven United Netherlands"). Though usually it's just called the "United Provinces" or "The Dutch Republic".

As shown above, "Nederland" (plural "Nederlanden") means low-lying country, so "Nederlanden" is really just another name for "Low Countries". This is why the Netherlands are called "Paises Bajos"/"Paises Baixos"/"Paesi Bassi"/"Pays-Bas" in Spanish/Portuguese/Italian/French; it is their translation of the meaning of the name.