Short answer: yes — that’s expected in Prefect 3.x today. Details: - Deployment-level

job_variables

overwrite work pool defaults at the field level. Since

env

is a single field (a dict), specifying

env

on the deployment replaces the pool’s entire

env

mapping rather than merging keys. - This is consistent with the docs language that deployment job variables “overwrite” work pool job template values. What to do instead: - If you want to keep the work pool’s environment variables and add one for a single deployment, either: - Don’t set

env

on the deployment; keep all env vars on the work pool, or - Include all of the pool env vars plus your extra var in the deployment’s

env

(i.e., fully specify the

env

dict at the deployment), or - Move the deployment-specific value into a Secrets/Blocks approach and reference it from your code so you don’t need to duplicate

env

. References: - Customize job variables (work pool vs deployment) - GCP worker guide (Cloud Run) If you’d like, share how you set the deployment

env

(UI vs

prefect.yaml

vs

.deploy

) and I can suggest the cleanest way to preserve the pool envs while adding your one-off variable.

Great find — yes, that issue does argue that deep-merge of job variables (including env dicts) is desirable: - Issue: Job variables should use a deep merge rather than shallow merge of dictionaries However, today that’s not how Prefect behaves. In current Prefect 3.x, deployment-level

job_variables.env

replaces the work pool’s

env

dict instead of merging keys. That’s why adding a single env var on the deployment appears to “erase” the pool’s env — the deployment’s

env

dict completely overrides the pool’s. This aligns with our docs that say deployment job variables “overwrite” pool defaults: - Customize job variables - GCP worker guide (Cloud Run) If deep-merge were implemented, your expected outcome (infra env from the pool + deployment-specific env working together) would “just work.” It’s a reasonable request; it just isn’t the current behavior. Workarounds/patterns you can use now: - Keep infra env exclusively on the work pool and avoid setting

env

on the deployment. Put deployment-specific config in Prefect Blocks/Secrets or parameters so you don’t have to touch the

env

dict at the deployment level. - If you must set

env

on the deployment, include both the pool envs and the deployment-specific keys in the deployment’s

env

(i.e., fully specify the dict). - If infra envs truly differ by deployment, consider separate work pools so you don’t need to merge. Quick question so I can tailor guidance precisely: are you on Prefect 3.x or 2.x? The behavior is effectively the same here, but #11041 was filed against 2.x. If you’d like, I can help file or upvote a 3.x-specific feature request to deep-merge job variables so envs compose intuitively.

Short answer: open a new 3.x issue and link to the old one. Why: - #11041 was filed against 2.x. The behavior you’re seeing in 3.x is “working as implemented” (deployment job_variables replace, they don’t deep-merge). A 3.x-specific feature request is the clearest way to track this. - In your new issue, link to #11041 for context and call out the desired deep-merge semantics. Helpful links: - Old issue for context: https://github.com/PrefectHQ/prefect/issues/11041 - Create new issue: https://github.com/PrefectHQ/prefect/issues/new/choose - Docs describing overwrite behavior: https://docs-3.prefect.io/v3/how-to-guides/deployments/customize-job-variables, https://docs-3.prefect.io/integrations/prefect-gcp/gcp-worker-guide What to include in the new issue (you can paste this): - Title: Deep-merge deployment job_variables.env with work pool env in Prefect 3.x - Version: Prefect 3.x (include exact version) - Worker: Cloud Run (or your worker type) - Current behavior:

Work pool base job template:
env:
  POOL_ONLY: "yes"
  SHARED: "pool"

Deployment job_variables:
  env:
    DEPLOY_ONLY: "true"
    SHARED: "deploy"

Observed at runtime: only DEPLOY_ONLY + SHARED=deploy. POOL_ONLY is missing.

- Expected behavior: - Deep-merge dicts so keys from the pool env are preserved and deployment keys override matching keys: - POOL_ONLY=yes, DEPLOY_ONLY=true, SHARED=deploy - Merge precedence: flow run > deployment > work pool - Rationale: Infra-level env vars differ from app-level env vars; replacing the whole dict makes composition cumbersome. - Prior art: link to #11041 If you share your pool template and deployment snippet here, I can help refine the issue text before you file it.