Water came in

Mark 4:37 (AV)
And there arose¹ a great storm² of wind³,
and the waves beat into the ship,
so that⁴ it was now⁵ full.

¹) Come into existence, begin to be.
²) The Greek word ‘lailaps’ used here points to a storm, or tempest. It is also used for a whirlwind. Anyway, it is a violent attack of wind, never a single gust nor a steady blowing wind, however violent, but a storm breaking forth from black thunder clouds in furious gusts, with floods of rain, and throwing everything topsy–turvy‭.
³) A violent agitation and stream of air‭; a very strong tempestuous wind‭.
⁴) In so much that‭.
⁵) Already

Other translations:

And a furious storm of wind [of hurricane proportions] arose, and the waves kept beating into the boat, so that it was already becoming filled. [AMP]

And a great windstorm arose, and the waves were breaking into the boat, so that the boat was already filling. [ESV]

A huge storm came up. Waves poured into the boat, threatening to sink it. [MSB]

And there arose a great storm of wind, and the waves beat into the ship, so that it was now full. [KJV]

A furious squall came up, and the waves broke over the boat, so that it was nearly swamped. [NIV]

But soon a fierce storm arose. High waves began to break into the boat until it was nearly full of water. [NLT]

And a great windstorm arose, and the waves beat into the boat, so that it was already filling. [NKJV]

Some further information:

And there arose a great storm of wind
“a tempest of wind.”
See Matthew 8:23-27, and Luke 8:22-25.

And the waves beat into the ship
Kept beating or pitching on the ship.

So that it was now full
Rather, “so that it was already filling.”
In Matthew ( Matthew 8:24 ), “insomuch that the ship was covered with the waves”; but this is too strong. It should be, “so that the ship was getting covered by the waves.”
So we must translate the word as used in Luke ( Luke 8:23 ) – not as in this Bible version – “And there came down a storm on the lake, and they were filled [with water]” – but “they were getting filled,” that is, those who sailed; meaning, of course, that their ship was so.

Observe that the storm was so great, that the ship was getting full of water (Mark 4:37), not by springing a leak, but perhaps partly with the shower, for the word here used signifies a tempest of wind with rain; however, the ship being little, the waves beat into it, so that it was filling up. 
Note, It is no new thing for that ship to be greatly hurried and endangered, in which Christ and his disciples, Christ and his name and gospel, are embarked.

Observe that this happened on the evening of the same day that he had preached out of a ship (probably the same ship as they sailed with), (Mark 4:35).
When He had been labouring in the word and doctrine all day, instead of re posing himself, he ex poseth himself, to teach us not to think of a constant remaining rest till we come to heaven.
The end of a toil may perhaps be but the beginning of a toss.

Observe that the ship that Christ made his pulpit is taken under his special protection, and, though in danger, cannot sink. What is used for Christ, he will take particular care of.

Observe that He himself proposed putting to sea at night, because he would lose no time; Let us pass over to the other side; for we shall find, in the next chapter, he has work to do there.
Christ went about doing good, and no difficulties in his way should hinder him; thus industrious we should be in serving him, and our generation according to his will.

Observe that they did not put to sea, till they had sent away the multitude, that is, had given to each of them that which they came for, and answered all their requests; for he sent none home complaining that they had attended him in vain. 
Or, They sent them away with a solemn blessing; for Christ came into the world, not only to pronounce, but to command, and to give, the blessing.

Observe that they took him even as he was, that is, in the same dress that he was in when he preached, without any cloak to throw over him, which he ought to have had, to keep him warm, when he went to sea at night, especially after preaching.
We must not hence infer that we may be careless of our health, but we may learn hence not to be over nice and solicitous about the body.

Observe that there were with him other little ships (Mark 4:36), which, no doubt, shared in the distress and danger. Probably, these little ships carried those who were desirous to go along with Christ, for the benefit of his preaching and miracles on the other side.
The multitude went away when he put to sea, but some were there, that would venture upon the water with him. Those follow the Lamb aright, that follow him wherever he goes. And those that hope for a happiness in Christ, must be willing to take their lot with him, and run the same risks that he runs. One may boldly and cheerfully put to sea in Christ’s company, even if we foresee a storm.

Now let us reflect on this

The Gospel of Mark tells us here of a life experience, which most of us will not be entirely alien to. The young people, whose ships of life were tossed about in the storm, have had similar experiences in their spiritual life as well.

Indeed, it can really storm our lives.
The weak man may well become afraid, when all the adversity, misery, and sorrow, that can terrify a human heart, come to him.

“All Your waves have passed over me,” says the poet. But he adds, “The Lord will command his mercy by day, and by night his song will be with me, the prayer to the God of my life.”

So he did not go down in that storm, and even the raging waves sang to him the song of the deliverances of God.

The same experience is also prepared for us, if we also lift up our eyes and hearts to Him who calms the storm, and comes to us when the soul’s need is greatest.

As the disciples of old, carried by the waves, we too meet the luminous consolation figure of the Son of Man, who calls out to us with his voice full of love, “It is I, do not be afraid.”
He may come when the night is almost over, just like before.
But if we continue to expect Him, then He will surely come.

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