Water comes from Samvartaka clouds. Samvartaka clouds are formed by Samvartaka fire which burns everything and evaporates all water in 3 worlds including some nether regions.
The process of Naimittika Pralaya is mentioned in detail in Chapter 45, Uttarabhaga of Kurma Purana and Chapter 3, Book 6 of Vishnu Purana. Both chapters mention same details with only difference that Vishnu Purana says Janardhana Vishnu turns into Rudra.
There are four Pralayas. Nitya, Naimitika, Prakrta and Atyantika. Chapter 45, Kurma Purana explains it as follows: (translated by Shanti Lal Nagar)
योऽयं सन्दृश्यते नित्यं लोके भूतक्षयस्त्विह।
नित्यः संकीत्र्यते
नाम्ना मुनिभिः प्रतिसञ्चरः॥६॥
The destruction of the living beings that is witnessed every day in
this world is called Nitya dissolution by the sages.
ब्रह्मनैमित्तिको नाम कल्पान्ते यो भविष्यति।
त्रैलोक्यस्यास्य
कथितः प्रतिसर्गो मनीषिभिः।। ७।।
At the end of the kalpa, the dissolution of three Worlds by Brahma
(due to his sleep at the end of his day), has been called as the
Naimittika dissolution by the learned sages.
महदाद्यं विशेषान्तं यदा संयाति संक्षयम्।
प्राकृतः प्रतिसर्गोऽयं
प्रोच्यते कालचिन्तकैः॥८॥
When the ultimate causes of the universe beginning with Mahat and
ending with Viśeşa undergo dissolution, it is called the Prakata
Pratisarga (natural dissolution) by those who ponder over Kāla.
ज्ञानादात्यन्तिकः प्रोक्तो योगिनः परमात्मनि।
प्रलयः प्रतिसर्गोऽयं
कालचिन्तापरैर्द्विजैः।। ९ ।।
The final absorption of Yogins into the Supreme Atman as a result of
the realization (Jiāna), the Watchers of the Kāla, call it the
Atyantika Pratisarga (ultimate dissolution).
Chapter 45 explains Naimittika Pralaya in detail.
At the end of 1000 Mahayugas, creator Brahma thinks to absorb all beings into His self. Earth is afflicted with drought and Seven Suns start burning earth and they dry up everything.
चतुव्यूंहसहस्रान्ते सम्प्रासे प्रतिसच्चरे।
स्वात्मसंस्थाः प्रजाः
कर्तुं प्रतिपेदे प्रजापतिः॥ ११॥
At the end of the thousand sets of four Yugas, when the time of
dissolution arrives, Prajapati Brahma, thought of absorbing all the
people in his own self.
ततोऽभवत्त्वनावृष्टिस्तीव्रा सा शतवार्षिकी।
भूतक्षयकरी घोरा
सर्वभूतक्षयंकरी। १२॥
Thereafter, for a period of a hundred years since that time, there had
been a terrific draught, as a result of which, all the living being
were destroyed.
ततो यान्यल्पसाराणि सत्त्वानि पृथिवीपते।
तानि चाग्रे प्रलीयन्ते
भूमित्वमुपयान्ति च॥ १३॥
O lord of the Earth, the beings on earth who are physically weak, got
destroyed first of all, and were reduced to Bhumi (become one with the
earth).
सप्तरश्मिरथो भूत्वा समुत्तिष्ठन्दिवाकरः।
असह्यरशिमर्भवति
पिबन्नम्भो गभस्तिभिः॥ १४॥
Thereafter, the sun with his seven rays, while rising becomes
unbearable with the blazing heat. Through them he drinks up all water
present on the earth.
तस्य ते रश्मयः सप्त पिबन्त्यम्बु महार्णवे।
तेनाहारेण ता दीप्त्वा
सप्तसूर्या भवन्त्युत॥ १५॥
In this way, the seven rays of the sun dry up the water from the
middle of the ocean. Thanks to this intake, they become brilliant and
change themselves into seven suns.
ततस्ते रश्मयः सस शोषयित्वा चतुर्द्दिशम्।
चतुर्लोकमिमं सर्वं दहन्ति
शिखिनो यथा॥१६॥
Then, those seven rays (the seven suns), dries up all the lokas in the
four directions and starts burning them like the fire.
व्याप्नुवन्तश्च ते दीप्ता ऊर्ध्वञ्चाधः स्वरश्मिभिः।
दीप्यन्ते
भास्कराः सप्त युगान्ताग्निप्रदीपिताः॥ १७॥
All the seven suns, by means of their rays penetrating into the upper
and lower parts of the earth, burn the earth like the fire of
dissolution.
ते सूर्या वारिणा दीप्ता बहुसाहस्ररश्मयः।
खं समावृत्य तिष्ठन्ति
प्रदहन्तो वसुंधराम्॥ १८॥
Thus suns, having been illuminated by the water (sucked by them), shed
forth thousands of rays, pervading the entire sky forcefully, and put
the entire earth in flames.
ततस्तेषां प्रतापेन दह्यमाना वसुन्धरा।
साद्रिनद्यार्णवद्वीपा
निःस्नेहा सम्पप्रद्यते॥१९॥
Thereafter, with the excessive heat of those suns, the burning earth,
is deprived of water over the mountains, in the rivers and the oceans
etc., besides the islands.
दीप्ताभिः सन्तताभिश्च रशिमभिर्वै समन्ततः।
अधश्चोद्र्ध्वञ्च
लग्नाभिस्तिर्यक् चैव समावृतम्॥२०॥
सूर्याग्निना प्रमृष्टानां
संसृष्टानां परस्परम्।
एकत्वमुपयातानामेकज्वाल भवत्युत। २१॥
As the burning rays of the sun are spread in all the directions,
covering all high and low regions, so powerfully and envelop
everything. In this way, due to the fire of the sun rays, all the
padarthas of the world are turned into a single mass of fire forming one fiery unit.
Samvartaka fire burns nether regions and other regions after burning earth.
स दग्ध्वा पृथिवी देवो रसातलमशोषयत्।
अधस्तात्पृथिवीं दग्ध्वा
दिवमूर्ध्वं दहिष्यति।। २९॥
The flaming fire, after burning the earth, dries up Rasatala as well.
After burning the lower part of the earth, it starts burning the
heaven above.
योजनानां शतानीह सहस्राण्ययुतानि च।
उत्तिष्ठन्ति शिखास्तस्य वह्नेः
संवर्त्तकस्य तु।। ३०॥
The flames of Sarinvartaka fire, rises upto the height of hundreds,
thousands and ten thousands of yojanas.
गन्धर्वाश्च पिशाचांश्च सयक्षोरगराक्षसान्।
तदा दहत्यसौ दीप्तः
कालरुद्रप्रणोदितः॥ ३१॥
With the inspiration of Kalarudra, these flames start burning the
Gandharvas, Pisacas, Yaksas, Nagas and the Raksasas.
Due to Samvartaka fire Samvartaka clouds rise.
अतो गूढमिदं सर्व तदेवैकं प्रकाशते।
ततो गजकुलाकारास्तडिद्भिः
समलंकृताः।। ३४॥
Thereafter, the vast and thick clouds known as Samvartaka, having
shapes of huge elephants, decorated with the groups of lightnings,
rise over the sky.
उत्तिष्ठन्ति तदा व्योम्नि घोराः संवर्त्तका घनाः।
केचत्रीलोत्पलश्यामाः केचित्कुमुदसन्निभाः॥३५॥
धूमञ्जवर्णास्तथा
केचित्केचित्पीताः पयोधराः॥
केचिद्रासभवर्णास्तु लाक्षारसनिभाः परे॥
३६॥
There arise in the sky the terrible Samvartaka clouds of world
destruction. Some of those clouds are dark resembling the blue lotus
flowers. Some of them are white like water-lily, some are of smoke
colour, some are of yellow colour, and some are of colour like a
donkey, Some of them of are of red colour like lac juice.
सङ्खकुन्दनिभाश्चान्ये जात्यञ्जननिभास्तथा।
मनः शिलाभाश्च परे
कपोतसदृशाः परे॥ ३७॥
Some of them are white like the conch or the lotus flowers, some are
like the finest variety of collyrium, some are of the colour of red
arsenic, white, others have the colour of a pigeon.
इन्द्रगोपनिभाः केचिद्वरितालनिभास्तथा।
इन्द्रचापनिभाः
केचिदुत्तिष्ठन्ति घना दिवि॥ ३८॥
Some of them appear like
glow-worms, some resemble the yellow orpiment. Some are like rainbows.
Such clouds rise up in the heaven.
These Samvartaka clouds fill the earth with waters.
ततस्ते जलदा घोरा राविणो भास्करात्मजाः।
सप्तधा संवृतात्मानं
तमग्नि शमयन्ति ते।। ४१॥
Then the clouds-beings the progeny of
the Sun, turning themselves into seven forms, extinguish the fire on
earth with the pouring of the rain water.
ततस्ते जलदा वर्ष मुञ्चंतीह महौघवत्।
सुधोरमशिवं वर्षं नाशयन्ति च
पावकम्॥ ४२॥
Like a flood water gushes out from them as rain. The
terrible and inauspicious rain destroys the fire,
अतिवृद्धं तदात्यर्थमम्भसा पूर्यते जगत्।
अद्भिस्तेऽम्भोऽभिभूतत्त्वादग्निः प्रविशत्यपः॥४३॥
Thus, with the pouring of the excessive rain, the earth was filled
with enormous quantity of water. On being thus overpowered by water
the fire merges into the Water.
नष्टे चाग्नौ वर्षशतैः पयोदाः क्षयसम्भवाः।
प्लावयन्तो जगत्सर्व
महाजलपरिस्रवैः॥४४॥
As a result of the rainfall showered by the clouds, the fire on earth
is completely extinguished in hundred of years. The flood envelops the
entire universe with huge currents of water.
Due to excessive rains, water overflows engulfing earth.
अतिवृद्धं तदात्यर्थमम्भसा पूर्यते जगत्।
अद्भिस्तेऽम्भोऽभिभूतत्त्वादग्निः प्रविशत्यपः॥४३॥
Thus, with the pouring of the excessive rain, the earth was filled
with enormous quantity of water. On being thus overpowered by water
the fire merges into the Water.
नष्टे चाग्नौ वर्षशतैः पयोदाः क्षयसम्भवाः।
प्लावयन्तो जगत्सर्व
महाजलपरिस्रवैः॥४४॥
As a result of the rainfall showered by the clouds, the fire on earth
is completely extinguished in hundred of years. The flood envelops the
entire universe with huge currents of water.
धाराभिः पूरयन्तीदं नोद्यमानाः स्वयम्भुवा।
अत्यन्तसलिलौघास्तु वेला
इव महोदधेः॥४५॥
In this way, at the instance of Brahma, the earth is filled with the
water, as the sea shore is submerged with excessive moving of the
oceanic waves.
साद्रिद्वीपा ततः पृथ्वी जलैः सञ्छाद्यते शनैः।
आदित्यरशिमभिः पीतं
जलमभ्रेषु तिष्ठति।। ४६॥
Slowly the earth with the mountains and islands is covered with water,
and the water soaked by the Sun-rays stays in the clouds.
पुनः पतति तद्भूमौ पूर्यन्ते तेन चार्णवाः।
ततः समुद्राः स्वां
वेलामतिक्लान्तास्तु कृत्स्नशः।।४७।।
The same water again is poured on earth and the oceans are so over
filled, that, they overflowing the seashores cause a deluge.
पर्वताश्च विलीयन्ते मही चाप्सु निमज्जति।
तस्मिनेकार्णवे घोरे
नष्टे स्थावरजंगमे। ४८।
योगनिन्द्रां समास्थाय शेते देवः प्रजापतिः।
चतुर्युगसहस्रान्तं कल्पमाहुर्मनीषिणः ॥४९॥
Even the mountains become submerged in water besides the earth, All
the mobiles and immobiles are destroyed. As a result of which lord
Brahmā, under the influence of Yoganidra' goes to sleep in the ocean.
The learned people consider the period a thousand cycles of four Yugas
aka Kalpa.
This is how water comes at end of Kalpa.
