To close the fluidic gate, you must fire a coherent beam of gravitons from your deflector dish into one of the "holes" that appears in the field and make the singulatity collapse in itself, sealing the gate, though it is logical to assume that soon another one would be opened. It is important to say that the "holes" appear following a chaotic pattern, so it is only possible to predict the location of the next "hole" just seconds before it opens, and they stay open for a fraction of a second.
Also, this can only be attempted when the gate is opening or closing. If a ship comes through it, you will not be able to seal the gate until it enters this transitory state again, and there is a risk for the ship travelling through the gate. If the energy configuration is not precise the ship may be destroyed instantly.
There is a very small possibility that the closing of the gate will cerate a subspace shockwave that might alter the Cochrane coefficient of this region and interfere with your warp capability, even rendering warp travel impossible in this area of space. Setting subspace beacons to emit a reversed subspace signal arround the gate, in case there is this subspace wave, should hold the shock wave to a very limited area of space that would have minimum effect on the development of the species on any nearby planet.