Managing RDS Aurora MySQL connections per user or database

You can define resource options per MySQL user and each application should use their own credentials.

• MAX_QUERIES_PER_HOUR
• MAX_UPDATES_PER_HOUR
• MAX_CONNECTIONS_PER_HOUR
• MAX_USER_CONNECTIONS

Example:

ALTER USER 'john'@'%' WITH MAX_QUERIES_PER_HOUR 90;

More details: Setting Account Resource Limits

Although this will limit the impact across applications, it will start failing once it hits these limits. If systems are truly independent and you don't have resource contraints, to reduce the blast radius ideally you'd create separate databases as you suggested to make sure there is no impact between each application, move towards a microservice architecture.