Large footprint and very low efficiency are main disadvantages of solar chimneys. To resolve this, solar desalination system has been added under the collector of a solar chimney power plant. Generally the collector ground is completely covered by the desalination pond but here it is shown that more benefit can be achieved by partial occupation of the collector area. This is performed by implementing the particle swarm optimization (PSO) algorithm in conjunction with a one dimensional simulation code. The code is first validated using data of a laboratory scale solar chimney. Then, optimization results show that for a collector diameter of 250 m and tower height of 200 m, a solar pond located between radii 85 and 125 m of the collector can maximize the outcome of the combined system. Generally, dimensions of the desalination system depend on local cost of building the system and price of electricity and fresh water produced.