Another interpretation: The Holy One, blessed be He, foresaw that Moses would be called "good" and was destined to be taken from the world by means of water. Therefore He did not write concerning the waters "that it was good."
Why the Waters Were Never Called Good
Yalkut Shimoni on Torah 5:10
דָּבָר אַחֵר צָפָה הַקָּדוֹשׁ בָּרוּךְ הוּא מֹשֶׁה קָרוּי טוֹב וְעָתִיד לִטֹּל אֶת שֶׁלּוֹ מֵעַל יְדֵי הַמַּיִם לְפִיכָךְ לֹא כָּתַב בָּהֶן כִּי טוֹב.