Heat generation and its impact on transport of polystyrene beads in the proximity of an optofluidic silicon photonic crystal resonator and nanophotonic standing wave array traps are studied theoretically and simulated numerically. The temperature rise in ambient water for photonic crystal resonator is calculated to be as high as 27 K and 2 K for nanophotonic standing wave array trap for 10 mW of input laser power of 1550 nm wavelength. The properties of optical trapping and biomolecular sensing of these devices are demonstrated to be strongly affected by the combination of buoyancy driven flow and thermophoretic drift of particles. Specifically, the region around the electromagnetic hot spot is depleted because of a high free energy barrier. Switching to 1064 nm laser wavelength and correspondingly using silicon nitride instead of silicon waveguide structure resulted in two orders of magnitude less potential energy that allows easier trapping of beads.