Even though Data Lakes are efficient in terms of data storage, they increase the complexity of query processing; this can lead to expensive query execution. Hence, novel techniques for generating query execution plans are demanded. Those techniques have to be able to exploit the main characteristics of Data Lakes. Ontario is a federated query engine capable of processing queries over heterogeneous data sources. Ontario uses source descriptions based on RDF Molecule Templates, i.e., anabstract description of the properties belonging to the entities in the unified schema of the data in the Data Lake. This thesis proposes new heuristics tailored to the problem of query processing over heterogeneous data sources including heuristics specifically designed for certain data models. The proposed heuristics are integrated into the Ontario query optimizer. Ontario is compared to state-of-the-art RDF query engines in order to study the overhead introduced by considering heterogeneity during query processing. The results of the empirical evaluation suggest that there is no significant overhead when considering heterogeneity. Furthermore, the baseline version of Ontario is compared to two different sets of additional heuristics, i.e., heuristics specifically designed for certain data models and heuristics that do not consider the data model. The analysis of the obtained experimental results shows that source-specific heuristics are able to improve query performance. Ontario optimization techniques are able to generate effective and efficient query plans that can be executed over heterogeneous data sources in a Data Lake.