Silicon-photonic networks on chip (PNoCs) provide high bandwidth with lower data-dependent power dissipation than does the traditional electrical NoCs (ENoCs); therefore, they are promising candidates to replace ENoCs in future manycore chips. PNoCs typically employ photonic waveguides with dense wavelength division multiplexing (DWDM) for signal traversal and microring resonators (MRs) for signal modulation. Unfortunately, DWDM increases susceptibility to intermodulation (IM) and off-resonance filtering effects, which reduce optical signal-to-noise ratio (OSNR) for photonic data transfers. Additionally, process variations (PVs) induce variations in the width and thickness of MRs causing resonance wavelength shifts, which further reduce OSNR, and create communication errors. This paper proposes a novel cross-layer framework called HYDRA to mitigate heterodyne crosstalk due to PVs, off-resonance filtering, and IM effects in PNoCs. The framework consists of two device-level mechanisms and a circuit-level mechanism to improve heterodyne crosstalk resilience in PNoCs. Simulation results on three PNoC architectures indicate that HYDRA can improve the worst case OSNR by up to 5.3× and significantly enhance the reliability of DWDM-based PNoC architectures.