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A channel aware particle filtering approach is proposed for target tracking in multi-hop wireless sensor networks. The quantized M-bit data are relayed through multi-hop fading channels in order to reach a fusion center. Each relay node employs a binary decision relay scheme where the relay output is inferred from the channel impaired observation received from its source node. The observation likelihood function is derived based on the characteristic of the channel fading and noise. For two cases where the fusion center has the knowledge of the instantaneous fading channel gains and where it has only the knowledge of fading channel statistics, we propose the channel aware particle filtering for target tracking. The improved tracking accuracy and robustness to channel imperfection of the proposed filter is shown through computer simulations.