"Water being contaminated from Zombie bodies when a river is used as a defensive feature.
1) You should have stored water inside the settlement encase of attack by raiders/zombies.
2) The water will flush/rinse/wash away the contamination. Once the corpses are removed don't use it for a few hours to a day
3) Use should be boiling and or treating/putrefying it before use anyways.

As for contamination on crops. Good point and could be a issue no matter where you place the crops. I agree the crops should be planted closer to the settlement. But still need a buffer zone of bare ground for a killing zone. Planting the rows so they away from the settlement to reduce cover for raiders and zombies to hide in.
Now if you build fences/barriers so it channels the zombies through patches between patches of crops. This way zombies will mostly stay in clear areas.
Now if zombies get into the crops wait till they exit to clear areas before killing them. Then you can back track the zombies path and destroy/sanitize them where contact/contamination is a problem.
Don't forget to fix any breaches they made so others can't fallow and contaminate the crops again.


"

"I'm bugging in. I live on/next to a family farm.

The dogs will be used for security as they are now.
The cats will stay the same as pest control.

They all are also companions/family so we will protect them."