Topological subsystem codes can combine the advantages of both topological codes and subsystem codes. Suchara et al. proposed a framework based on hypergraphs for construction of such codes. They also studied the performance of some subsystem codes. Later Bravyi et al. proposed a subsystem surface code. Building upon these works, we propose efficient decoding algorithms for large classes of subsystem codes on hypergraphs and surfaces. We also propose a construction of the subsystem surface codes that includes the code proposed by Bravyi et al. Our simulations for the subsystem code on the square octagon lattice resulted in a noise threshold of 1.75%. This is comparable to previous result of 2% by Bombin et al. who used a different algorithm.