The climate of Earth has been roughed up quite a bit last century. But it has no idea what it's got coming with this portal of yours.
Earth turns into Venus.
Update: As R.M. pointed out, the amount of energy is not 'maybe a long term thing', it's the Major Issue. This has been fixed now.
How much water are we talking?
Let's say your portal is 10km below sea level. Dropping from that pressure to pressure at sea level gives a flow speed of somewhat over 400 meters per second: $\sqrt{10^4\mathrm{m} \cdot 10 \frac{\mathrm{m}}{\mathrm{s}^2} \cdot 2}$ (water is incompressible so we can just use potential energy). This is well over the speed of sound, or comparable to the speed of a typical handgun bullet.
This 400 m/s flow is though the entire portal, $\pi \cdot 5000^2 = 7.9 \cdot 10^7 \mathrm{m}^2$, for a total of about $30 \cdot 10^9 \mathrm{m}^3$ of water per second, that's a cube of water about 3 km or 2 miles on a side per second.
Comparing that to other rivers. The discharge of your portal is about 100 000 cubic kilometers per hour, or about three times the the amount of water discharged by all of Earth's rivers in a year.
Comparing it to a lahar, a very destructive mud flow. These can be 100 meters deep and run at 'several tens of meters per second'. If the stream from your portal would turn into a lahar of 50 meters deep, it would be 2000 km wide. If we were to slow it down to a mere 40 meters per second (as fast as a car going over the speed limit), that would require it to be again 10 times as wide, so 20 000 km. Sailing around the entire African continent is only slightly more than that. So the entire African coast would turn into an extremely destructive mud flow of almost 50 m deep. Given that there are mountains to the south of the Sahara, the mud flow will probably be much deeper and mostly to the North.
At this point most of my assumptions are starting to break down. I assumed the effect on the ocean surface would not be too great. It will likely be a giant maelstrom tens or maybe even hundreds of kilometers across. This means the amount of water flowing through it is going to be somewhat less. Let's cut it by a factor 10, so $30\cdot10^8 \frac{\mathrm{m}^3}{\mathrm{s}}$.
The volume of Earth's oceans is about 1.3 billion cubic kilometers. There are about 30 million seconds in a year, so that's about 90 million cubic kilometers per year. So it takes about 15 years for the portal to cycle through the equivalent of all the water.
What happens to that water?
The specific heat of water is about $4 \frac{\mathrm{J}}{\mathrm{kg \cdot K}}$, so it takes about 4 kilojoules to heat a Liter of water 1 degree Celsius. That's about 4 MJ to heat a cubic meter 1 degree. The potential energy in dropping a cubic meter of water from 10 km up is about 100 MJ, so you're going to heat up your water about 25 degrees by slamming it high speed into the sand (or, quite quickly, other water).
This means that, if the Earth's energy loss from radiation would stay the same, in about 15 years all the water would have cycled through the portal once and the ocean would, on average, have heated up 25 degrees. Another 45 years and all the water will be boiling.
Water has a latent heat of about $2.3 \frac{\mathrm{MJ}}{\mathrm{kg}}$, or $2300 \frac{\mathrm{MJ}}{\mathrm{m}^3}$. So it then takes a few centuries for all the water to boil off and turn into vapor.
What will happen to all that energy?
Normally, the Earth radiates away energy as long wave, or infra red radiation. Greenhouse gases like carbon dioxide reflect this radiation back at us.
There is a lot of carbon dioxide stored in the oceans, around 60 times that of the pre-industrial atmosphere. However, if water is heated, it can't store as much carbon dioxide. Water of about 30 degrees Celsius can store only about a third of what water of 4 degrees can store. This is actually much more complicated than dividing by a third.
So, if all the oceans heat up 25 degrees, the carbon dioxide in the atmosphere is going to increase by factor of 10 or so. We've managed to increase it by about 50% or so in the last hundred years.
To add to this, warmer water evaporates more readily, and water vapor is also a very strong greenhouse gas.
This means that the Earth wouldn't cool nearly as fast as it normally would.
And, at some point, maybe after a few years, maybe after several decades, even if you were to turn off the portal, the increased greenhouse gases and incoming energy from the Sun will will cause a runaway greenhouse effect and turn Earth into Venus.
Who dies first?
The first creatures to die is probably a fish being blasted into an unlucky scorpion at high speed. After that anything going through the portal will die. Next to go is anything within a few hundred kilometers of the Mariana Trench and anything in Northern Africa.
Europe and the rest of Africa will soon (within hours? days? weeks?) follow. The shortest path from the Saharan portal back to the Mariana Trench is through the Himalaya's, so my guess is the water will mainly flow through Africa towards the Southern Atlantic and through Southern Europe the Eastern part of Africa and the Arabian Peninsula into the Indian Ocean. Everything in its way will die.
So the America's, most of Asia and Australia will likely not flood. Australia is closest to the Mariana Trench, so the weather there will turn weird after a day. It will take probably take a few days for the effects of the sudden change of energy distribution to be transported by the jet steam towards the America's and the remaining parts of Asia, so they've got maybe another week before the freak weather begins (think hurricanes, extreme rainfall, etc.). Some animals and some humans in those parts of the world could possibly survive this for a few years.
Some speculation on what would happen if the water didn't heat up:
The remaining flow is still a good 20 times the amount of water the Gulf Stream transports at its peak, so I would wager all ocean currents stop doing what they're doing and start flowing towards the South-West Pacific.
This means no more warm water flowing to the North Atlantic so that's a new ice age for Europe. Similar goes for Japan.
Most of North Africa is going to get flooded, I have no clue what that will do with the climate. This water is going to be under 10 degrees Celsius, so it'll cool down equatorial areas by a lot.
The giant maelstrom around the Mariana Trench is going to cause a lot of mixing in the Pacific Ocean, so most of that ocean is going to be a lot colder than it was before.
All of this cold water near the surface everywhere will mean that the Earth will radiate away much less energy and that there will be much less energy to drive atmospheric processes.
The internal ocean water however will heat up on average.