My son is 16 months old and his dad was sent to prison today how bad will it affect him?

At 16 months a child probably won't even remember their dad very well. The important thing will actually be about maintaining the relationship between the boy and his father. Obviously I don't know how long his father will be in jail for, but men who go to war or work overseas often arrive home and have difficulty bonding with their children. If the child has contact with the father over this period that problem will be mitigated. Children need to have honesty and clarity about what is going on to make sense of it, but at 16 months that is probably less necessary. Try to bring a positive male role model into the boy's life, like a grandpa if possible.