If you use silicone from the hardware store be sure to use a CLEAR Window and Door variety. The danger is when you use a silicone that is designed for kitchens or bathrooms. Often times there is a mildew resistant compound they mix in with the silicone for kitchen and bath that is TOXIC for fish!
Typically we are using silicone (RTV) on skimmer face plate and waterfall weir spillways. On our bottom drains we use a POLYURETHANE Sealant. It is for roof & flashing.
I don't know the brand off the top of my head but the variety we use when dry has a bit of flexibility. Maybe you can make it out from the photo. There are polyurethane sealants that dry hard as a rock and those are the ones you want to stay away from! You will see them names Construction Adhesive Polyurethane. The need for the flexibility allows for slight movement of the Earth, settling of soil, expanding and contracting from weather and such.
Attachment:
Bottom Drain Sealant 917.jpg
The Pond Digger