Despite the existence of obstacles in many database applications, traditional spatial query processing assumes that points in space are directly reachable and utilizes the Euclidean distance metric. In this paper, we study spatial queries in the presence of obstacles, where the obstructed distance between two points is defined as the length of the shortest path that connects them without crossing any obstacles. We propose efficient algorithms for the most important query types, namely, range search, nearest neighbours, e-distance joins, closest pairs and distance semi-joins, assuming that both data objects and obstacles are indexed by R-trees. The effectiveness of the proposed solutions is verified through extensive experiments.