In this paper, we introduce a novel FPGA-based methodology for accelerating SQL queries using dynamic partial reconfiguration. Query acceleration is of utmost importance in large database systems to achieve a very high throughput. Although common FPGA-based accelerators are suitable to achieve such a high throughput, their design is hard to extend for new operations. Using partial dynamic reconfiguration, we are able to build more flexible architectures which can be extended to new operations or SQL constructs with a very low area overhead on the FPGA. Furthermore, the reconfiguration of a few FPGA frames can be used to switch very fast from one query to the next. In our approach, an SQL query is transformed into a hardware pipeline consisting of partially reconfigurable modules. The assembly of the (FPGA) data path is done at run-time using a static system providing the stream-based communication interfaces to the partial modules and the database management system. More specifically, each incoming SQL query is analyzed and divided into single operations which are subsequently mapped onto library modules and the composed data path loaded on the FPGA. We show that our approach is able to achieve a substantially higher throughput compared to a software-only solution.