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During lagoon treatment and storage, anaerobic processes contribute to emission of volatile compounds, some of which are offensive odors. Therefore, there is major interest in developing swine manure treatment systems that can substantially reduce malodor emissions from lagoons. The effect of two pre-treatments of liquid swine manure on odor was tested for three months after a 12-month operation of a pilot study to evaluate lagoon conversion to a storage pond. The study consisted of comparing side by side the effect of solid-liquid separated effluent and a new advanced system (solid-liquid separation followed by biological N treatment) on odor reduction in liquid of converted lagoons. As a control, an anaerobic lagoon regularly loaded with raw manure was included in the study. Lagoon liquid was sampled bi-weekly for water quality and odor analysis. Treatment effect on odor abatement was estimated by olfactometry and analysis of five selected malodor compounds (phenol, p-cresol, p-ethylphenol, indole, and skatole) by gas chromatography/mass spectrometry in lagoon liquid samples. Water quality improvements with respect to the anaerobic lagoon control (such as reduction of suspended solids, chemical oxygen demand, and nitrogen concentrations) were moderate with solid separation alone but very significant with the biological N pre-treatment. These water quality improvements paralleled the malodor reduction analytical results. Solid-liquid separation alone reduced about 72% of malodor compounds in lagoon liquid, but odor panel tests showed no significant difference in odor intensity with respect to the control (P > 0.05). The greatest odor compound reduction of about 99% with the biological N pre-treatment was also detected by the odor panel with a significant odor intensity reduction with respect to the control (P < 0.05). The remarkable improvement of water quality in the converted lagoon showed the additional environmental benefit of reducing malodors when an advanced treatment technology is retrofitted to a swine operation with an existing anaerobic lagoon.