Water level in connected tanks I've got two water tanks on my rooftop(both tanks are of exactly same dimensions and are at exact same level) connected at the bottom. I fill them via an external pipe connected with a pump on the first floor. In order to fill the tanks, I open the lid of one tank (Tank 1) only so little as I can insert a pipe inside the tank. 
After I've inserted the pipe I put some weight (a brick) on the lid so that the pipe does not come out of the tank due to water pressure. Please note that the lid on the other tank (Tank 2) remains closed. Tank 1 is also partially open (just a bit as there's a pipe inserted). 
After some time of  filling the water, I checked the water levels in both the tanks and I noticed a significant difference in the water levels(I opened the lid of both tanks to check the water level). 
I'm confused because since the tanks are connected at the bottom, I was expecting both of them to have the same water level at all points of time. Why am I wrong? Can the rate with which the external pipe is filling Tank 1 be greater than the rate at which the water is going from Tank 1 to Tank 2 (via the connecting pipe)?
 A: *

*If the lid on Tank2 is airtight, then the air pressure will build up
in Tank 2 and prevent the water inflow into Tank 2 from the bottom
(via Pipe 2).

*If the lid on Tank2 is NOT airtight then:


*

*If the water flow through Pipe 1 is more than 2x greater, than the flow through Pipe 2, then Tank 1 will have a higher water level when the pump is ON.  After the pump is turned OFF, the water levels will equalize eventually.

*If the water flow through Pipe 1 is NOT more than 2x greater, than the flow through Pipe 2, then the tanks will always have the same water level



The water flow depends on the pressure differential between the two pipe ends, divided by the resistance of the pipe to the water flow.  For practical purposes, the resistance of the pipe to the water flow depends on the crossectional area of the pipe and the length of the pipe and its bends and kinks.

Note: The pressurized air in Tank 2 will affect the pressure differential between Pipe 2 ends and consequently will affect the water flow in that pipe.  If that pressure differential falls down to zero, the water will stop flowing altogether.
A: As george mentioned the difference in level of water in both tanks depend on many factors like the pressure difference,pump capacity and the height of water level in tank 1.
I assume that both lids 1 and 2 are not air sealed practically.
Then the water flow will depend on the height of water level in tank 1. 
Pressure difference given as P= (densitygh).
Now based on bernoulis equation this pressure head is converted into velocity head meaning 
p/(density*g) = v^2/(2*g).
Now we know that the mass flow rate Q = (density * v * A).
Where v is velocity and A is cross sectional area of pipe.
Now generally when we consider a pipe many loses like frictional losses,bending losses,etc will all arise which eventually reduce the velocity by almost half of it.
Now if the pump capacity is  greater than the flow rate from 1 to 2 then tank 2 takes a lot of time.
If you could know the exact specifications of your pump along with the specifications of pipes that you are using you can calulate all this.
Hope this helps you.
