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Normally, you can use any conduits/pipes (eg. EnderIO, Thermal Expansion/Dynamics, ExtraUtilities2, Buildcraft) to pump water in, but it'll depend on what version of minecraft and what pack you're using.
Haven't played Continuum so don't know whether recipes are 'vanilla' or not, but from a quick look at the modlist you've at least got conduits from Thermal Dynamics and pipes from ExtraUtilities2. You'll need a water 'generator' of some kind (aqueous accumulator maybe).
I ended up using Immersive Engineering pipes to get water in to my Carpenter and into an Advanced Tank on my EFAB. Used the IE Pump over a 1x3 water pool.
Kept both topped off at all times.
I had a huge misunderstanding of the pump I was using sense I thought it only needed one water source but however needed an infinite water source. But thanks for letting me know how you got it to work.