A rural dairy farm located on the island of Oahu, Hawaii needed to upgrade current lagoon treatment system for further reuse as floor flushing and crop irrigation. This is a comprehensive bench scale and pilot plant study to evaluate the potential biological treatment and reuse systems. Systems evaluated include: (1) pre-existing lagoon system, (2) integrated anaerobic BIO-NEST/aerobic EMMC (entrapped mixed microbial cell) system, (3) aerobic EMMC reactor only system. Based upon a comprehensive economic evaluation and sensitivity analysis, the EMMC-only system achieved the best effluent quality for simultaneous removal of carbon and nitrogen. The pilot study of the EMMC-only reactor achieved an overall of 78% TCOD, 63% SCOD, 65% TN, and 96% soluble NH3-N removal efficiencies (HRT 12 h, continuous aeration). Implementing this system would cost about $0.25 a cow/day to remove a ton of organic TCOD ($88.10/cow/year). The information presented provides a model for animal producers to consider in evaluating alternatives to upgrade existing waste management facilities.