Moving, aerated water discourages mosquito growth. You'll want to make sure the water in your natural pool is constantly being pumped from the swimming area into the regeneration zone and back again. This movement will make it much less likely that mosquitos will take a liking to your pool, let alone want to lay their eggs there.
If mosquitos do become a problem, make sure that your water is being circulated properly. Your regeneration zone should provide an ideal home for mosquito-predating critters, so make sure that its thriving as well.
