The microbiological and physicochemical characterization of samples from the different wastewaters generated during oil extraction in a continuous olive mill was performed. The main aim was to determine which of the physicochemical parameters were the best fitted to correctly characterize these residual waters. High correlations were obtained for COD, DOC, K, P and N contents with the sampling points, allowing the distinction of olive washing waters (OWW) from olive centrifuge waters (OCW) and olive mill wastewaters (OMW). These parameters were sufficient for a rapid and less costly chemical characterization of these waters. Phenols and oil and grease contents, together with low pH and dissolved oxygen contents, and high organic loads, were the most toxic for microbial populations. Microbial characterization showed that fungi were well adapted to these stressing environmental characteristics and the reuse of OMW after aerobic treatment with microbial species isolated from the effluent is considered.