Allocating initial water rights is a prerequisite for implementing water rights trading and enhancing the water use efficiency. This paper investigates the establishment of a model for allocating basin-wide initial water rights considering both the quantity and quality of water. First, a new concept, two-dimensional water rights, is presented and described in the paper. Second, the initial water rights allocation model, which maximizes the harmonious degree of an entire water system, is developed based on five principles: (1) the basic water demands, (2) fairness, (3) respect for the status quo, (4) economic efficiency, and (5) the unification of water withdrawals and sewage discharge. Third, the proposed model is applied to the Beijiang River Basin in southern China, and the model validity and reasonability of the presented two-dimensional water rights allocation scheme are verified via comparisons with other allocation patterns. Finally, several conclusions are presented.