A fluid from a fermentation process or the like is passed or circulated through chambers of a bipolar membrane electrodialysis unit to separate an ionizable organic acid stream and at least one co-ion or residual stream. The organic acid stream is preferably concentrated (e.g., by recirculation, dewatering or both), and a product is recovered from the concentrated stream, for example by crystallization, and other outputs from the electrodialysis unit may be integrated with overall treatment and applied elsewhere in the treatment system. Depleted feed may be returned upstream to enhance yield, condition the medium or form a by-product. Treatment systems of the invention may replace a cation exchange bed and/or various filter arrangements, and recirculation of the feed and product flows through the unit enhance recovery, separation and quality of the target species. An ED chamber may include a filling of ion exchange beads to maintain a desired operating efficiency as the feed is depleted, and the straight-through operation effectively operates as pre-filtration stage to provide downstream product-bearing flows with processing characteristics for enhanced treatment, recovery and product quality. When operated to treat a downstream waste, systems allow additional recovery of value in the form of product, unexpended nutrients, co-factors and/or other components present in the waste.