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This survey paper focuses on the estimation schemes in molecular communication (MC) systems. The existing studies in estimation schemes can be divided into parameter estimation (e.g., distance, diffusion coefficient, and flow velocity) and channel estimation. In this paper, we present, for the first time, a comprehensive survey on i) distance estimation, since distance is the most widely estimated parameter in current studies, ii) estimation of other parameters (i.e., the parameters excluding distance), and iii) channel estimation that focuses on the channel impulse response (CIR). Moreover, we examine the noise that may impact on the estimation performance and the metrics applied to evaluate the performance of different estimation schemes. Numerical results are provided to compare the performance of different distance estimation schemes. In addition, future research directions in parameter estimation and …