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Probably the best control for flies, grubs, and other damaging insects, is poultry. Most fowl will eat bugs, and think they have been given a treat. Our Muscovies have been great at this, cleaning out our grasshopper plague in a matter of days. Guinea Fowl, and Chickens are also pretty good at it, as are most other ducks. Extra protein too, saves on your feed bill.
Some organic gardeners use Diatomaceous Earth. It is a single celled sea creature, which is crushed. It feels like talc, looks like fine, tan dust. When small insects ingest it, or move over it, it can cause cuts that lead to death. Some people use it to control the spread of worms in animals also, by sprinkling it on the ground where the animals leave their droppings.
We experienced moderate success with it, using it on broccoli and cauliflower in the Yakima Valley. It didn't stop the cabbage loopers, but ours were smaller than any of the neighbor's were.
It is less likely to work with sucking insects, than with chewing insects. If the insect ingests it, it is more effective.
There are many other pest controls that are labeled as "organic", but remember, just because it is Organic, or Natural, does not mean it is harmless. Some of the natural pest controls are still dangerous to humans.
A dish of beer is probably still one of the more effective ways to deal with slugs. And tomato collars don't kill anything, but may stop tomato worms from destroying your crop.
Deer can be kept out by a 6 foot fence that cannot be seen through. Deer won't jump into an unknown situation, so if they can't see it, they won't go. Blood meal sprinkled around the plants also repels deer- but it does have to be reapplied every few weeks or after rain (Miracle Gro Organic Fertilizer will also do the trick).
One of the best pest controls is to rotate your crops as much as possible, and to plant things together that naturally repel the pests. Marigolds reputedly repel some insects. Mint also repels some pests. Rotating crops helps to keep infestations from building up year after year due to existing presence in the soil.
The old myth that well tended gardens repel pests better than ill tended ones, isn't quite true. They simply can survive more of an onslaught, if they are healthier to start with.