© 2004 by CRC Press LLC. There are many kinds of coastal water quality issues. They arise from various sources of inputs to the coastal zone that are either chronic or accidental. Pollution of seawater mostly results from a) point source and diffuse pollution originated from agricultural, industrial and urban activities, or b) pollution from maritime activities, e.g. waste oil as well as all types of toxic substances being dumped into the sea, including radioactive ones (Kershaw, 1997). Toxic phytoplankton blooms are a new plague. Although they are not the direct result of human behaviour, they are probably linked to human activities, and particularly contaminated ballast water. These harmful disruptions have severe effects on shellfish stocks, entailing long production shutdowns. Problems also currently exist with open sewers discharging into places designated for shellfish production or into recreational waters (Boelens et al., 1999). After flooding, there is run-off pollution from agriculture and urban areas and nitrate concentrations and bacterial counts increase remarkably. The increase in nitrate concentrations can lead to dramatic eutrophication, whereas pathogenic bacteria can make aquaculture products hazardous to human health (Lees, 2000). Other activities or phenomena such as dredging, deep water sludge disposal or landfill seepage are concerns for water quality and marine living resources (Sullivan, 2001). While hydrodynamic modelling results and the handling of geo-referenced information are becoming more readily available to coastal management stakeholders within GIS (Geographic Information Systems), there is still a lack of direct interfacing of model results with baseline mapping data (BASIC, 2001). This paper discusses solutions to bridge this gap and illustrates them with two case studies where effective model outputs are being used for improved environmental management and decision-making.