If the bottom is flat and smooth you could glue pieces of plastic over the holes using a suitable adhesive.

Epoxy a plate larger in diameter than the bottom of your container to your container and let it cure for a week. You might like to include a small solar fountain in your water feature.

If your holes are not too big, I would look in my local DIY store for plastic items such as screw caps/corks there are lots to choose from such as 'Hole Plugs Plastic Blanking Inserts' or Vacuum Flask Screw Cap Stoppers and of course plastic water butts have stoppers to fill the holes you dont want a tap in so its worth a look.

I'm not sure what you could use to act as a plug/Bung but clear waterproof sealant is good, or what about a small piece of pond lining to go inside?

I wished I had thought of that Dan, great idea and the liner could turn any container of almost any shape and size into a minature pond!

Yes! We're doing one for our front garden! A glazed terracotta pot!

You could seal the liner to the side of the pot/container. Some people staple and sometimes nail them but I don't like that Idea because the liner could pull down and tare (that's just my opinion though)

Yes the container is to have a solar pump.we miss the sound of water in the garden. I did see an idea in a book where someone had put a half barrel inside a large pot, they filled the gap between the barrel and pot with compost and planted water loving plants in it. I must admit it was very effective.

Sounds fab!