Kerala, like every other nature centric destination becomes even more green and beautiful in Monsoon. Kerala is one destination where it does not rain too much. There is intermittent shower, there are spells, but nothing that would actually hamper progress of an itinerary.
Monsoon is a season when good quality resorts offer off-season rates and so a lot of guests arrive with a view to enjoy resort facilities / amenities / luxuries.
Plantation Highlands - It gets even mistier in monsoon and climate even more pleasant. Tourists are fewer especially in weekdays and drives lovelier. For honeymooners and getaway seekers who arrive without a fixed plan and good time in hand this is ideal to just let things flow. If its raining harder, sit back and enjoy it from the room balconies, if it just drizzling, just walk around or go out for a drive for a bit of sightseeing / exploring.
Backwaters - Nothing changes in Backwaters in Monsoon via a vis winter except a bit of humidity. However there is little doubt that the backwaters and the area around are at its scenic best in monsoon. One could just opt for a lakeside luxury resort and avail bargain prices or one explores backwaters in a houseboat or via a homestay, sans humidity everything else is picture perfect.
Beach - Marari, Kovalam and Poovar. All beach options but different as chalk and cheese. Marari, a fisherman's village. Monsoon is when the beaches get even more idyllic and resorts offer bargain prices. Excellent time for an Ayurveda Getaway or where idea is just to get cut off. One can easily combine a stay with the Alleppey backwaters / Kumarakom Lake.
Standalone Getaways - Athirapally falls at about 50 kms from Cochin Airport are at their best during Monsoon and therefore is a very popular local getaway. Thattekad, again at about 50 kms from Cochin Airport is an excellent nature centric getaway. Though its not the best time for Bird watching but boating, plantations and overall feel of the area makes for a good getaway.