What material are you using for the water effect? Most cure over time, allowing you to take care of bubbles before the product fully sets. Tapping the base sharply and repeatedly can help dislodge them, allowing them to rise to the surface, where they can be popped with a fine pin. If done early enough, the "water" is still sufficiently liquid to self-level and fill the void the bubble would otherwise leave.
As for clinging to the foot, do you fully fill the void under the model's feet or are they sitting on top of rough basing? Bubbles will naturally cling to what they can (feet, in this case), but you may be inadvertently creating air pockets that are exacerbating the issue. Lots of tapping should dislodge them for popping, but filling the voids with putty or the like before pouring would remove that source, altogether.
Also bear in mind that the thinner the layers poured, the more manageable they become. If you're doing a lot of bases/larger scenery pieces and using a 2-part resin, it may be worth spreading the mix across a larger number/surface, but in thinner layers (to be repeated until the desired depth is achieved). "Pour, dry, done" products mean you don't have to worry about batch size, since you don't have to gauge the amount to mix, so you can use thin layers without any wastage, even on a single small base.
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