Reservoir-based dielectrophoresis (rDEP) is a recently developed technique that exploits the inherent electric field gradients at a reservoir-microchannel junction to focus, trap, and sort particles. However, the locally amplified electric field at the junction is likely to induce significant Joule heating effects that are not considered in previous studies. This work investigates experimentally and numerically these effects on particle transport and control in rDEP processes in PDMS/PDMS microchips. It is found that Joule heating effects can reduce rDEP focusing considerably and may even disable rDEP trapping. This is caused by the fluid temperature rise at the reservoir-microchannel junction, which significantly increases the local particle velocity due to fluid flow and particle electrophoresis while has a weak impact on the particle velocity due to rDEP. The numerical predictions of particle stream width and electric current, which are the respective indicators of rDEP manipulation and fluid temperature, are demonstrated to both match the experimental measurements with a good accuracy.