Surface water and groundwater are intrinsically connected, such as in low elevation areas like coastal plains with phreatic aquifers. In urban areas, inter-related issues regarding water resources, land use, and urban policies are particularly important. This chapter presents a spatial approach for identification of the most susceptible areas to flooding and appropriate measures to minimise it, based on urban and hydrologic criteria, using a geographic information system as a spatial decision support system. Knowledge modelling in this decision-making process is the most crucial part of the approach because it considers the expertise of various professionals, policies, regulations, and other determinants and helps to structure all decision-making data and rationale. The analysis of the Brazilian case comes with more significant challenges that involve legal and technical aspects of urban planning and water management in a spatial analysis approach. Results show that a closer relationship between urban planners and water managers in coastal cities should help in land-use planning actions and policies for avoiding problems, such as floods and saltwater intrusion in coastal aquifers, and stimulating interdisciplinary urban planning teams as an essential condition for urban environmental management as well for the resilience of present and future cities.