Much of Dr Watkins' research focuses on ethical questions arising from the wrongs of the past. In some of his recent writings, he has examined the nature and value of forgiveness, particularly in deeply divided societies. He is currently working on the ethics of reparation, both in the context of ordinary interpersonal relationships and at the level of institutional responses to human rights violations.

He has broader research interests in both moral theory (especially moral luck, moral responsibility and deontological ethics) and philosophy of law (especially philosophy of international law).