The bacteria content of a little water is insignificant. Your main host for bacteria is rock and sand, not water.
Definately lower the salinity with water changes (these are the easy kind). Do you have anything alive in the tank?
Like the above post said, whats the salinity level? The salinity should be around 1.020-1.025. It is quite easy to lower, you just take out some (not very much) of the tank water then replace it with freshwater.