The soil covering your tortoise burrow works hard to divert rain and also to hold some water and then allow it to evaporate. Continued or heavy rains can overwhelm the soil’s water-holding capacity causing soggy soil and possible flooding.
When you see rain coming, you can cover the burrow with a tarp or heavy plastic sheet being sure that the water will drain away from the burrow as it runs off the tarp. Since high winds often accompany rain, have some 2x4s or rocks handy to weight down the tarp.
Remove the tarp as soon as the rain ends to avoid creating a greenhouse effect. Moisture in the soil can then begin to evaporate again. Never leave a burrow covered for an extended period of time.