Genesis 6:16

Go thou unto Phison, and take from thence a precious stone, and fix it in the ark to illuminate you: with the measure of a cubit (or span) shalt thou complete it above. And a door shalt thou set in the side of the ark; and with dwelling-places, inferior, second, and third, shalt thou make it.

בצדה תשים, on the side which is wide, for that is the side called צד. The long side is referred to as צלע.

תחתיים, the lower deck in ships; as in any other ship, the customary lower deck.

שניים ושלשים, they are similar, parallel to the lower deck.

צהר, this word is derived from the word צהרים, “noon,” an instruction that Noach make a window in the ark that would let in the light after the rain would stop falling, during the long period when the water level would gradually subside. This is what is meant in 8,7 when the Torah wrote ויפתח נח את החלון, “Noach opened the window.” Some of our sages (Bereshit Rabbah 31,11 ) believe that Noach suspended a brilliant gemstone which provided light inside the ark. The words תעשה לתבה, “you shall construct for or inside the ark,” contradict such an explanation. There is no question that Noach had prepared oil for the lamps he took along into the ark. The window mentioned here in our verse is a natural source of light, affixed by Noach in the highest part of the ark.

ואל אמה, to the uppermost cubit of the slanting roof of the ark. It is called thus seeing that at the top there was no more than one cubit of width between the roof sloping down on one side and that sloping down on the other side. The purpose of the slanting roof was to let the rain run off the ark.

ופתח התבה, the entrance/exit which was closed after everybody who was entitled to enter the ark had entered it.

תחתים, a lower deck; the letter י in this word serves a dual purpose, a) to represent the plural mode of the word, as well as 2) a letter describing a relative and not an absolute position. When speaking of the third deck, שלשים, the letter י which would reflect the relative position is unnecessary (seeing it was the top, i.e. highest deck) so that we do not find the dagesh in the י in that word. The י describing the plural mode does appear, just as it does in words such as נכרים, gentiles, or in מצרים, Egyptians. In Bereshit Rabbah 31,11 we are told that the lower deck served as the container of refuse, the middle deck as the accommodation for the family of Noach and the pure animals, [the ones fit as sacrifices], whereas the upper deck served as accommodation for the impure species of animals. Some scholars believe that the lowest deck accommodated the ritually impure species of animals, the middle deck was reserved for Noach and his family as well as for the ritually pure animals, whereas the top deck was for the refuse. Noach constructed sort of a trap door through which he shoveled the refuse.

ואל אמה תכלנה מלמעלה, “and finish it to within a cubit from the top;” this was meant to prevent the rains from getting into the ark and causing its planks to rot. If you were to argue that the rains then could cause the width of the ark to start rotting, we refer you to the commentary of Rabbi Joseph Kara, who understands the subject in the verse to be the window. This window should be affixed in the upper cubit near the roof, the cover of the ark.