Maintain your yard by removing any branches, dead leaves, rock piles and stacks of firewood that chipmunks and red squirrels could use as shelter. Also, make sure bird feeders are high above the ground and that no seed spills down.
Put up chicken wire around your garden to keep the red squirrels and chipmunks from entering and eating your plants. They should not try to return once they have no food source.
Purchase a repellent that contains ammonium soap, bitrex and Thiram. Apply it to areas where the chipmunks and red squirrels show up. Such repellents are not the most effective way but they are helpful at repelling the pests for a short amount of time.
Use live traps that can be purchased online or at home and garden stores. Mix sunflower seeds with peanut butter and place it in the trap. Set the trigger on the steel box traps after two or three days when the pests are used to going inside the box.
Place a sheet over the trap after you have caught the chipmunks or red squirrels. Make sure you have permission to release the animals to wherever you relocate them.