The example has:

apiVersion: v1
kind: Pod
metadata:
  name: secret-env-pod
spec:
  containers:
  - name: mycontainer
    image: redis
    env:
      - name: SECRET_USERNAME
        valueFrom:
          secretKeyRef:
            name: mysecret
            key: usernamekey
      - name: SECRET_PASSWORD
        valueFrom:
          secretKeyRef:
            name: mysecret
            key: passwordkey
  restartPolicy: Never

the above from:

https://kubernetes.io/docs/concepts/configuration/secret/

I've created a secret like this:

kubectl --namespace=mycustomnamespace create secret generic mysecret --from-literal=passwordkey="abc123" --from-literal=usernamekey="mememe"

I understand that the above secrets exist under the namespace.

But if I try this:

apiVersion: v1
kind: Pod
metadata:
  name: secret-env-pod
  namespace: mycustomnamespace
spec:
  containers:
  - name: mycontainer
    image: redis
    env:
      - name: SECRET_USERNAME
        valueFrom:
          secretKeyRef:
            name: mysecret
            key: usernamekey
            namespace: mycustomnamespace
      - name: SECRET_PASSWORD
        valueFrom:
          secretKeyRef:
            name: mysecret
            key: passwordkey
            namespace: mycustomnamespace
  restartPolicy: Never

(note that I added a namespace declaration under metadata)

I get this error:

Error validating data: [ValidationError(Pod.spec.containers[1].env[2].valueFrom.secretKeyRef): unknown field "namespace" in io.k8s.api.core.v1.SecretKeySelector, ValidationError(Pod.spec.containers[1].env[6].valueFrom.secretKeyRef): unknown field "namespace" in io.k8s.api.core.v1.SecretKeySelector];

If I take out the namespace(s) (under the secretKeyRef(s))....the pod fails..with

Warning Failed 2s (x8 over 1m) kubelet, minikube Error: secret "mysecret" not found

Yes, my secrets are in the namespace:

kubectl get secrets --namespace mycustomnamespace

NAME                  TYPE                                  DATA      AGE
default-token-55bzp   kubernetes.io/service-account-token   3         10m
mysecret              Opaque                                2         10m

APPEND : (resolution)

It was an error on my part. Check my comment under Vasily's answer.

But basically, the magic-sauce is that the below yml....

metadata:
  name: secret-env-pod
  namespace: mycustomnamespace

the above yml should "drive" the namespaces (aka, set the scope of the namespace) for the rest of the configuration (yml) ....

(if you are a future reader of this question, double and triple check that you have everything under the correct namespace. ALL of your normal "get" statements need to use -n (aka --namespace) as a part.

example

kubectl get pods

the above will only get pods under "default".

you have to do

kubectl get pods --namespace mycustomnamespace