bibharṣi śuklaṁ khalu varṇam ātmanaḥ
sargāya raktaṁ rajasopabṛṁhitaṁ
kṛṣṇaṁ ca varṇaṁ tamasā janātyaye
Vasudeva prayed to the Lord, “You are called śuklam. Śuklam, or ‘whiteness,’ is the symbolic representation of the Absolute Truth because it is unaffected by the material qualities. Lord Brahmā is called rakta, or red, because Brahmā represents the qualities of passion for creation. Darkness is entrusted to Lord Śiva because he annihilates the cosmos. The creation, annihilation and maintenance of this cosmic manifestation are conducted by Your potencies, yet You are always unaffected by those qualities.” As confirmed in the Vedas, harir hi nirguṇaḥ sākṣāt: the Supreme Personality of Godhead is always free from all material qualities. It is also said that the qualities of passion and ignorance are nonexistent in the person of the Supreme Lord.
In this verse, the three colors mentioned — śukla, rakta and kṛṣṇa — are not to be understood literally, in terms of what we experience with our senses, but rather as representatives of sattva-guṇa, rajo-guṇa and tamo-guṇa. After all, sometimes we see that a duck is white, although it is in tamo-guṇa, the mode of ignorance. Illustrating the logic called bakāndha-nyāya, the duck is such a fool that it runs after the testicles of a bull, thinking them to be a hanging fish that can be taken when it drops. Thus the duck is always in darkness. Vyāsadeva, however, the compiler of the Vedic literature, is blackish, but this does not mean that he is in tamo-guṇa; rather, he is in the highest position of sattva-guṇa, beyond the material modes of nature. Sometimes these colors (śukla-raktas tathā pītaḥ) are used to designate the brāhmaṇas, kṣatriyas, vaiśyas and śūdras. Lord Kṣīrodakaśāyī Viṣṇu is celebrated as possessing a blackish color, Lord Śiva is whitish, and Lord Brahmā is reddish, but according to Śrīla Sanātana Gosvāmī in the Vaiṣṇava-toṣaṇī-ṭīkā, this exhibition of colors is not what is referred to here.
The real understanding of śukla, rakta and kṛṣṇa is as follows. The Lord is always transcendental, but for the sake of creation He assumes the color rakta as Lord Brahmā. Again, sometimes the Lord becomes angry. As He says in Bhagavad-gītā (16.19):
tān ahaṁ dviṣataḥ krūrān
kṣipāmy ajasram aśubhān
āsurīṣv eva yoniṣu
“Those who are envious and mischievous, who are the lowest among men, are cast by Me into the ocean of material existence, into various demoniac species of life.” To destroy the demons, the Lord becomes angry, and therefore He assumes the form of Lord Śiva. In summary, the Supreme Personality of Godhead is always beyond the material qualities, and we should not be misled into thinking otherwise simply because of sense perception. One must understand the position of the Lord through the authorities, or mahājanas. As stated in Śrīmad-Bhāgavatam (1.3.28), ete cāṁśa-kalāḥ puṁsaḥ kṛṣṇas tu bhagavān svayam.