Whenever it rains heavy the basement shower drain backs up with clean water and also the toilet rises and bubbles. Where is the water coming as I'm not flushing or running any water in the house. Please help! Thank you.

Barbee
This means you have rainwater draining into the sanitary sewer.
If the sewer is partially blocked, when it rains the water coming from the weeping tiles or roof leaders overloads the system and backs up at the lowest point. Usually a basement floor drain but if the floor drain is covered it will come up in the shower.
Its rainwater so that explains why it is clear.
The answer is to snake out the main drain leaving the basement. You can rent a snake but I would check with the municipality if your on municipal sewers.
Some municipalities will come out and snake it for you. If not call a plumber.
Happens all the time and is usually not a serious problem.

Barbee, just a thought before you spend money on repair. Check with several of your neighbors to see if their basement level drains back up too. You did not mention it but are you on city sewer or septic tank. In my town so many people have illegally hooked their gutters and sump pumps to the city sewer that we all get some backup during heavy rains. The city inspected every home on our block this week looking for illegal hook ups.