As per AWS billing dashboard I see a higher cost as "EC2: NAT Gateway - Data Processed", is there a way I can get bottom to this, which instance or which user or which s3 bucket or which emr cluster?
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A NAT Gateway will be attached to a specific VPC so this resource usage can be scoped to that, in addition a NAT Gateway is bound to route table(s) in a VPC.
By using this you can identify the subnets in which resources that are using the NAT Gateway are residing, if you have multiple NAT Gateways CloudWatch metrics exist that will allow you to get a breakdown of the BytesIn and BytesOut.
From here you could enable VPC flow logs on the selected subnets and then analyse the transit that is occurring perhaps using Athena to query your logs.

Chris Williams
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We have only one VPC, is there any simple way in billing dashboard, Simple filter we can apply and see which EC2 used it, or which subnet used it. – Jaishree Mishra Sep 29 '20 at 14:43
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Unfortunately not as the billing is on the NAT not the EC2 host – Chris Williams Sep 29 '20 at 15:08
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He is correct, See this link as well https://aws.amazon.com/premiumsupport/knowledge-center/vpc-find-traffic-sources-nat-gateway/ – Jaishree Mishra Sep 30 '20 at 20:40