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There is no charge for those specific traffic flows. Even though the EC2 pricing page mentions that cross-AZ traffic generally incurs charges, the same page also makes an explicit exception for traffic between S3 and EC2 instances in the same region: https://aws.amazon.com/ec2/pricing/on-demand/#Data_Transfer_within_the_same_AWS_Region
Data transferred directly (see endpoints) between Amazon S3, Amazon EBS direct APIs*, Amazon Glacier, Amazon DynamoDB, Amazon SES, Amazon SQS, Amazon Kinesis, Amazon ECR, Amazon SNS or Amazon SimpleDB and Amazon EC2 instances in the same AWS Region is free. If other AWS services are in the path of your data transfer, you will be charged their associated data processing costs. These services include, but are not limited to, PrivateLink endpoints, NAT Gateway and Transit Gateway.
Note specifically that you should have a VPC gateway endpoint for S3 in your VPC and attached to your VPC's route tables that will be accessing S3. Traffic passing through an S3 gateway endpoint is not charged. If you haven't got the gateway endpoint, your traffic will typically go through a NAT gateway, and NAT gateways charge for all traffic passing through them, regardless of destination.
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