Security Groups in AWS are used to control inbound and outbound traffic at the instance level within an Amazon VPC. They act as a virtual firewall for EC2 instances to regulate traffic. Network ACLs, on the other hand, are used at the subnet level and not primarily for individual instances. Route tables are used to control the routing of traffic between subnets and the Internet, but do not directly control traffic at the instance level. Amazon GuardDuty is a threat detection service, not a traffic control mechanism.