To determine the net effective permissions in AWS, three key elements are taken into account: AWS IAM groups, AWS IAM roles, and AWS service control policies (SCPs). IAM groups aggregate permissions for users by attaching policies that grant or deny permissions. IAM roles grant permissions through policies to entities that assume the role. Service control policies are used in AWS Organizations to manage permissions across all accounts in the organization. All three of these components together help calculate the net effective permissions for a user or a service.