First you need to figure out if the phlegm is from sinus drainage or if it is originating in her bronchial tubes. If she has sinus drainage and/or congestion there are numerous things to eliminate: virus, sinus infection (viral or bacterial), allergies (which typically at this age they are too young to test for and get a positive result due to the minute amount of histamines in the blood and lack of necessary blood volume for accurate testing), ear infection, upper respitory infection isolated to the bronchial tubes, lung infection...
Is there congestion? Nasal or chest?
First thing i would do if you are not already, is get a cool mist vaporizer or if you have the funds, get a high quality air purifier and humidifier (there are humidifiers on the market that are also air purifiers). Second, at night, rub medicated chest rub on the bottoms of her feet with loose socks on, this will aid in relieving congestion. You can get local honey (after age 1 it is said to be safe by the majority of the medical community) and make sure it is local, and feed her a teaspoon a day. If she has sore ears, you mince garlic in olive oil, warm it (NOT hot) and place a few small drops in her ears to sooth her ears. (Ear issues often cause sinus issues). The garlic is a natural antibiotic and the oil will sooth a sore ear as well as soften any wax if there is overproduction from illness.
Please provide more info regarding her symptoms. I am not a doctor, but my 2.5 year old has had issues since she was an infant and I have done tons of research, taken her to an allergist, numerous visits with her pediatrician, gotten endless advice from herbalists, other mothers and about 5 or 6 different nurses who are also mothers. I will NEVER advise you to do anything that could be dangerous to your child's health.