There is no given information on when or how often it rains, but there are routes where it rains more often then elsewhere. The two routes reported to be more rainy are Route 14 and Route 8.
For other generations the time it will rain is more specific, but in Gen VI it just says "some days"
Don't quote me on this but I think Rain dance might be able to make it rainy, too. But if you plan on evolving Sligoo it will not work, because it needs to be natural rain.
You can also make it rain by changing the 3DS date and time, it's better explained in this video.
Hope I helped.