Green water in turtle tanks is often a result of algae which in itself isn't particularly harmful. However, it's important to examine the conditions in the tank that can lead to an overgrowth of algae as they may indicate other issues that could be potentially harmful. Anytime you have water issues (cloudy or smelly water, or high ammonia or nitrate levels), the first things to assess are your tank size and filtration methods.
Conditions That Promote Algae
Algae tends to grow well in turtle tanks because of the amount of waste turtles produce which acts as nutrients for the algae. First, make sure the turtle is in a large enough tank -- a tank that's too small can lead to waste products that are highly concentrated and perfect for algae growth. As a general rule, the tank should hold at least 10 gallons of water per inch of turtle - even larger is better. This means a full grown turtle needs a tank larger than 100 gallons. If the tank is too small, water quality will be much harder to maintain, and the health and well-being of your turtle is at risk.
Finding the Right Filter
A very powerful filter is the next step, preferably a canister type filter rated for a tank three to four times the size of your actual turtle tank; turtles really are messy and need the extra filtration. (A pet store can help you choose one.) Feeding the turtle in a separate container can also help reduce the amount of waste in the water that can lead to algae growth.
When you clean the filter, don't disinfect it or use really hot water to clean it, because you don't want to kill the beneficial bacteria it harbors. The good bacteria is needed to degrade the turtles' waste products.
Make sure the lights on your turtle tank are not on for too long. The lights should be on for 12 hours or so per day; if they are on longer they may contribute to algae growth (not to mention stressing your turtle).
Don't be tempted to cut the lighting too much though -- while the lights do contribute to algae growth, proper lighting (both basking and UVA/UVB) is critical to your turtle's health. However, if the tank receives any direct sunlight, moving it out of the light can help significantly.
Keeping the tank clean is vital to water quality and will help with the algae (see Keeping your Turtle Tank Clean for help). "Dilution is the solution to pollution" as the saying goes. Keep in mind there may always be some algae in the tank and perhaps even on your turtle's shell -- trying to totally remove algae is futile and unnecessary. The goal is to keep the algae under control, but more importantly, make sure the water quality is good.
You can also add in animals that eat algae like snails and plecostomuses. However, your turtle might eat them so you'll have to replace them continuously.