Let X be a projective K3 surface over C. We prove that its Cox ring has a generating set whose degrees are either classes of smooth rational curves, sums of at most three elements of the Hilbert basis of the nef cone, or of the form 2(f+f′), where f,f′ are classes of smooth elliptic curves with f⋅f′=2. This result and techniques using Koszul's type exact sequences are then applied to determine a generating set for the Cox ring of all Mori dream K3 surfaces of Picard number three which is minimal in most cases. A presentation for the Cox ring is given in some special cases with few generators.