Scarcity and value of fresh water has increased use of desalination technologies and alternative water sources globally. This paper briefly discusses the areas that affect the costs and identifies the areas which are believed to have been mainly neglected so far and that require specific attention in terms of future R&D. They are feed water and system characterization, process optimization and concentrate management. R&D and advances in feed water and system characterization is required for determining the fouling potential of the RO modules and as such for establishing a proper pre-treatment system and advancing process optimization as well as concentrate management. This paper highlights the importance of interactive and hydrodynamic effects in water and in system characterization from a fundamental point of view; it discusses the need for developing characterization techniques based on theoretical principles combined with computational and analytical techniques for eventual use by the end-users.