InfluxDB and Flux can be used to scale Kubernetes deployments by annotating HPA resources with a Flux query that controls scaling based on data within InfluxDB. The process involves deploying InfluxDB, Metrics Adapter, and Telegraf in a custom namespace, configuring Telegraf to collect metrics from an Nginx deployment, and using pkger to create a bucket for storing metrics. A HorizontalPodAutoscaler is then created with an annotation that specifies a Flux query to fetch the waiting field from the nginx measurement, which triggers scaling events when the value exceeds zero.