In Bereishis 1:9 it says וַיֹּאמֶר אֱלֹהִים יִקָּווּ הַמַּיִם מִתַּחַת הַשָּׁמַיִם אֶל מָקוֹם אֶחָד וְתֵרָאֶה הַיַּבָּשָׁה , And God said, "Let the water that is beneath the heavens gather into one place, and let the dry land appear". Rashi explains: שהיו] שטוחין על פני כל הארץ והקוום באוקינוס], They were spread out over the surface of the entire earth, and He gathered them in the ocean. Why did the water need this special prompting from God? Why didn't the water simply follow the laws of nature, and flow down to the lowest place (the seabed)?
Tol'dos Yitzchak (by Rav Yitzchak Karo, uncle of the Bes Yosef) suggests that the water and continents were combined at first as a muddy slush, and this command separated them, with the land portion coming together (and rising) to form the continents and the water portion coming together (and sinking) into the space between the continents. In his words:
נאמר שלפי שהיה התהום שהיה מים ועפר כמו מים עכורים גזר השי״ת שיקוו המים שהם גבוהים אל מקום שפל למטה ושיעלה העפר למעלה ושניהם הפך טבעם זה עולה וזה יורד
the vilna gaon says this is a remez to kriat yam suf (splitting of the red sea) where the waters retreated and the "dry land" appeared. i.e. the wet ground became dry as the midrash says. forgot the exact source.
pshat could also mean some of the water retreated to the tehom (deep) as we see regarding the flood that the tehom opened up and flooded the world along with the rain (Genesis 7:11 "on that day all the springs of the great deep burst forth, and the floodgates of the heavens were opened")
Perhaps the land mass was completely covered by water and after the command the land mass rose up and differentiated itself from the water that previously covered it.
Or, the water had a significant amount of turbulence such that the land mass was regularly covered by the water. After the command the waves calmed down and the land mass was visible.