This paper reviews some of the current water quality issues relating to the surface waters of Scotland and highlights some of the key issues likely to be significant over the next decade. The sustainable management of water quality requires an appreciation of the temporal and spatial assessment of the resource, together with an identification of reference or natural conditions from which to determine change, and the elucidation of the drivers of change. Only through this integrated approach, can appropriate management strategies be developed and prioritised, bearing in mind that impacts may be decoupled from sources in both time and space. This paper highlights recent trends in water quality (from a hydrochemical perspective) with separation into three broad groups: rivers, lochs and estuaries. For rivers, a general reduction in concentration of determinants that are more indicative of urban point sources (phosphorus, ammonium, suspended solids, biochemical oxygen demand etc.) is apparent, while in more agriculturally-dominated areas, an increase in concentration of solutes that are considered more diffuse in origin, (e.g. nitrate) is reported. The increasing contribution to total loads from diffuse pollutants is a priority area for both research and policy. Current scientific challenges are to define the most appropriate spatial context within which regional water quality issues can be monitored and managed. It is likely that future emphasis will be placed on making an initial ecoregion based grouping in conjunction with physically defined catchment, which will be used to quantify site-specific impacts. Such an organisational approach will provide a mechanism that enables a targeted monitoring strategy to be developed. This will allow the establishment of ecologically based targets for water quality, and an improved understanding the biogeochemistry of pollution reversibility and ecosystem recovery. It is also fundamental to the development of tools through which to predict the time scale and magnitude of any recovery, such that environmental benefit can be optimised against realistic socio-economic constraints. The inter-relations between water quality objectives and the development of legislation for water resources management in Europe are discussed.