The existence of scaling and concentrate discharges has always been a challenge for the development and improvement of reverse osmosis (RO) facilities. Scaling is also a main reason that does not enable us to increase recovery and reduce concentrate discharge, as the deposition of sparingly soluble salts due to supersaturation has a negative effect on membrane performance. The presented research has focused on scale formation and crystallization theory studies that can provide efficient control of crystal formation and growth. As a result, a new technology is developed that reduces concentrate flow by 20–100 times, escapes scaling, and reduces reagent consumption. Calcium carbonate and calcium sulfate are deposited without the use of softening reagents but due to supersaturation provided by brine concentration with membranes. This reagent-free technology is a result of a combination of low-rejection nanofiltration (NF) membranes and knowledge of the basic laws of crystallization process theory. Experimental results are presented that demonstrate the conditions necessary to start the nucleation process in the concentrate flow and evaluate nucleation and crystal growth rates. Examples of the application of the new technology for ground and seawater desalination are presented and discussed. The technology allows not only to reduce concentrate discharge but also to separate it into a number of concentrated solutions such as sodium chloride, magnesium sulfate, and magnesium chloride. An economic comparison of the new approach compared to conventionally operated RO systems widely used for groundwater treatment is provided.