Both the current trends in technology such as smart phones, general mobile devices, stationary sensors and satellites as well as a new user mentality of utilizing this technology to voluntarily share information produce a huge flood of geo-spatial and geo-spatio-temporal data. This data flood provides a tremendous potential of discovering new and possibly useful knowledge. In addition to the fact that measurements are imprecise, due to the physical limitation of the devices, some form of interpolation is needed in-between discrete time instances. From a complementary perspective - to reduce the communication and bandwidth utilization, along with the storage requirements, often the data is subjected to a reduction, thereby eliminating some of the known/recorded values. These issues introduce the notion of uncertainty in the context of spatio-temporal data management - an aspect raising an imminent need for scalable and flexible data management. The main scope of this thesis is to develop effective and efficient techniques for similarity search and data mining in uncertain spatial and spatio-temporal data. In a plethora of research fields and industrial applications, these techniques can substantially improve decision making, minimize risk and unearth valuable insights that would otherwise remain hidden. The challenge of effectiveness in uncertain data is to correctly determine the set of possible results, each associated with the correct probability of being a result, in order to give a user a confidence about the returned results. The contrary challenge of efficiency, is to compute these result and corresponding probabilities in an efficient manner, allowing for reasonable querying and mining times, even for large uncertain databases. The paradigm used to master both challenges, is to identify a small set of equivalent classes of possible worlds, such that members of the same class can be treated as equivalent in the context of a given query predicate or data mining task. In the scope of this work, this paradigm will be formally defined, and applied to the most prominent classes of spatial queries on uncertain data, including range queries, k-nearest neighbor queries, ranking queries and reverse k-nearest neighbor queries. For this purpose, new spatial and probabilistic pruning approaches are developed to further speed up query processing. Furthermore, the proposed paradigm allows to develop the first efficient solution for the problem of frequent co-location mining on uncertain data. Special emphasis is taken on the temporal aspect of applications using modern data collection technologies. While the aforementioned techniques work well for single points of time, the prediction of query results over time remains a challenge. This thesis fills this gap by modeling an uncertain spatio-temporal object as a stochastic process, and by applying the above paradigm to efficiently query, index and mine historical spatio-temporal data.