Pour water and salt into a medium pot and bring to a rolling boil over high heat. Once the water is boiling, stir in the shell pasta, and return to a boil. Cook the pasta uncovered, stirring occasionally, until the water has cooked down a bit, about 5 minutes.
Stir in the milk, and continue boiling for another 5 minutes. Add the Cheddar, Parmesan, pepper, and mustard; stir until the cheese melts and the sauce is thick and creamy. The starch from the pasta thickens the sauce as the pasta cooks.
