diff --git a/src/prefect/workers/base.py b/src/prefect/workers/base.py
index fdce809e30ae..b3ee5a1f4c3a 100644
--- a/src/prefect/workers/base.py
+++ b/src/prefect/workers/base.py
@@ -930,7 +930,12 @@ async def _get_configuration(
 
         deployment_vars = deployment.job_variables or {}
         flow_run_vars = flow_run.job_variables or {}
-        job_variables = {**deployment_vars, **flow_run_vars}
+        job_variables = {**deployment_vars}
+
+        # merge environment variables carefully, otherwise full override
+        if isinstance(job_variables.get("env"), dict):
+            job_variables["env"].update(flow_run_vars.pop("env", {}))
+        job_variables.update(flow_run_vars)
 
         configuration = await self.job_configuration.from_template_and_values(
             base_job_template=self._work_pool.base_job_template,
diff --git a/tests/workers/test_base_worker.py b/tests/workers/test_base_worker.py
index 97a1fc9407e6..7a91d6b6b530 100644
--- a/tests/workers/test_base_worker.py
+++ b/tests/workers/test_base_worker.py
@@ -18,7 +18,7 @@
 )
 from prefect.flows import flow
 from prefect.server import models
-from prefect.server.schemas.core import Flow, WorkPool
+from prefect.server.schemas.core import Deployment, Flow, WorkPool
 from prefect.server.schemas.responses import DeploymentResponse
 from prefect.settings import (
     PREFECT_API_URL,
@@ -1644,3 +1644,34 @@ def create_run_with_deployment(state):
 
         worker.run.assert_awaited_once()
         assert worker.run.call_args[1]["flow_run"].id == flow_run.id
+
+
+async def test_env_merge_logic_is_deep(prefect_client, session, flow):
+    deployment = await models.deployments.create_deployment(
+        session=session,
+        deployment=Deployment(
+            name="env-testing",
+            tags=["test"],
+            flow_id=flow.id,
+            path="./subdir",
+            entrypoint="/file.py:flow",
+            parameter_openapi_schema={},
+            job_variables={"env": {"test-var": "foo"}},
+        ),
+    )
+    await session.commit()
+
+    flow_run = await prefect_client.create_flow_run_from_deployment(
+        deployment.id,
+        state=Pending(),
+        job_variables={"env": {"another-var": "boo"}},
+    )
+    async with WorkerTestImpl(
+        name="test",
+        work_pool_name="test-work-pool",
+    ) as worker:
+        await worker.sync_with_backend()
+        config = await worker._get_configuration(flow_run)
+
+    assert config.env["test-var"] == "foo"
+    assert config.env["another-var"] == "boo"