[1] The adjective "deep" is here feminine, baqei=a, probably presupposing the noun krh/nh "spring". The headword itself, mela/nudros, is an epic epithet of springs. See e.g. Homer, Odyssey 20.158: "twenty women went to the black-watered spring" (ai( me\n e)ei/kosi bh=san e)pi\ krh/nhn mela/nudron). Same or similar entry in other lexica (see the references at Photius mu221 Theodoridis), and cf. the scholia to Homer, Iliad 9.14 (another "black-watered spring").
[2] i.e. the water looks black from its depth. See LSJ s.v. (= web address 1 below).