1. - Any plants already affected can't be salvaged. Pull them out and destroy them - Do not put them in the compost and don't leave them lying around . Burn them or put them in sealed plastic bags and get em out of the area. 

2. - Soil immediately surrounding the root area - loose soil in the hole from which the plant was just removed - should also be disposed of.

Preventative measures , some people say are like closing the barn door after the animals have escaped. But they certainly will help prevent a recurrence.

Female flies lay their eggs in moist loose soil, such as from newly planted seed rows. Covering seedbeds with floating row covers immediately after seeds are sown can help prevent an infestation.

Beneficial nematodes are very effective in controlling root maggots.

Turn under crop debris immediately after harvest to destroy overwintering sites.
 

Blueberry maggots    

The blueberry maggot (Rhagoletis mendax Curran) is a common pest of blueberries in Canada and the northern United States. Although its range seems to be expanding southward, infestations tend to be localized and sporadic in the South. The adult is a small, black fly, about 4 mm (3/16 in.) long .  It can be recognized by a distinctive pattern of black bands running diagonally across each wing , by white bars on each side of the thorax, a white spot at the posterior tip of the thorax, and white lines along the back edge of each abdominal segment. Larvae develop entirely within the blueberry fruit and grow to about 1/2 in. in length. They have tapered, wormlike bodies with no legs, eyes, or antennae .

"Use bait traps to trap adult blueberry maggots. Ammonium carbonate is the attractant, and the flies are caught on surfaces coated with tangletrap . There are several ways to design the traps. For one trap, start with a cottage cheese container. Place about 1 teaspoon of ammonium carbonate [a small vial of  liquid ammonia will suffice] in paper and faster it to the bottom of the container, then coat the inside walls with tangletrap . Hang the trap upside-down from the foliage by a string fastened to the bottom of the container. If you paint the trap goldenrod yellow, it will be even more effective."  - Michigan State University - Blueberry Maggot Fact Sheet

University of Maine -Monitoring for the Blueberry Maggot
 

Pepper Maggot   

The adult pepper maggot fly is a a brightly colored yellow striped fly . It has one pair of brown-banded, clear wings. A small black dot is located on each side of the last segment of the abdomen. The white, crook necked-shaped egg is roughly 2 mm long and about 0.3 mm wide. White and opaque when newly hatched, it turns yellow as it develops. Infestations of pepper maggot can be patchy and sporadic even in locations where there is a history of the insect infestations. To reduce populations, sanitation and crop rotation is helpful. Pick up any fallen peppers and destroy them. Destroy any horse-nettles (an alternate host) in the vicinity.

Once flies have been detected, there are several control methods available. One method is to cover the pepper plants with fine netting, sealed by dirt on the ground. This physically excludes the fly. The approach can only be effective if there is no possibility of adult flies emerging from the soil underneath the plants.

beneficial nematodes are another option. Nematodes are active pepper maggot larva seekers and move quickly through the soil.

If natural controls prove ineffective Malathion is recommended

Connecticut agricultural experiment Station-Pepper Maggot

North Carolina Cooperative Extension Service-Pepper Maggot

Cabbage Maggot

A very destructive early season pest is the cabbage maggot . This pest not affects you guessed it ... cabbage, and can also wreak havoc on other members of the Brassica family ...cauliflower, broccoli, brussel sprout, as well as radish, turnip, and beets.


The adult resembles the common house fly ,only a bit smaller, being about a quarter of an inch in length. The fly is a darkish ash gray and has black stripes on the thorax as well as black bristles over the body [Image]. The female will lay eggs which will hatch into white, legless maggots. These maggots feed on the roots of the previously mentioned vegetables. The maggots will develop into brown egg shaped puparia which are to be found from one to four inches down in the soil . During the winter period the maggot lives in the soil, The presence of  beneficial nematodes and Diatomaceous Earth in the soil at this point will severely retard the advance of this pest.
 

 As Spring comes around and the soil warms up, the adult will emerge from the ground and begin to mate. Eggs will then be laid on the soil close to the host plant. After about a week the eggs will hatch and the tiny maggots will begin feeding on the roots . They tunnel through the roots destroying them. Within a month the maggots will turn into a pupae and two to three weeks later the adult will come forth and the cycle begins again.

If natural controls prove ineffective Malathion is recommended

University of California - IPM Cabbage Maggot

The Cabbage Root Maggot in Newfoundland and Labrador
 

Seed Corn Maggot    

The pale yellowish-white seed corn maggot burrows into seeds already in the soil. Sprouts of several vegetable crops are attacked by this seed infesting maggot.  The Adult Fly looks pretty much like a common house fly... slight size difference.

Although it is called seed corn maggot it is much more likely to damage beans, peas, cabbage, turnip , onion, radish and spinach. It is a close relative of the onion maggot and the cabbage maggot.

The seed corn maggot passes the winter in the soil in the maggot stage inside a dark brown, cocoon-like puparia, 1 1/2 to 2 inch long.

The first-generation flies emerge about planting time. These flies are grayish-brown to slightly greenish in color and about 1/5 inch long. The flies deposit their eggs in the soil where there is an abundance of decaying organic matter , or on the seed or young, developing plant. The second and third generation appear in mid- and late summer.

The hatching maggots make their way to the sprouting seeds where they bore into, feed on, and often destroy the cotyledons and growing point of the seed of young plants.

Seed corn maggot populations vary greatly depending on environmental conditions , take precautions prior to planting to keep damage from this insect to a minimum. Otherwise, this critter will probably not be detected until seeds and seedlings are lost.
Plant in a seedbed only deep enough for adequate soil moisture.

Plant after the ground is warm enough for rapid germination and growth.

Reduce use of organic fertilizer in the seeded row, whenever possible, if and only if there has been a problem in the past with these pests.
 

One control option is to plant seeds pretreated with a product containing diazinon,  if unavailable, granules may be worked into the soil before planting.

Penn State Dept. of Entomology Fact Sheet

Perdue University- Field Crops

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