Human settlements in both arid lands and cities must, of necessity, alter hydrological regimes and geomorphology to provide clean, reliable drinking water, water for agriculture, and protection from flooding. Additionally, people also create substantial modifications to provide water for manufacturing, recreation, aesthetics, and sense of place. All of these practices can result in elimination or degradation of existing aquatic ecosystems, as well as creation of new ecosystems such as artificial lakes, stormwater retention basins, mitigation wetlands, groundwater recharge ponds, etc. Here we present a case study of the types of aquatic ecosystems in the Central Arizona – Phoenix LTER project area, noting the mix of extant, “restored”, and de novo ecosystems. We contend that, within the extreme ecosystem of a desert city, all aquatic ecosystems are, to a certain extent, designed. A deeper integration of ecology and design, along with clarification of the values and needs of the public, will enable scientists, policy makers, planners, and managers to maintain, create, and manage a suite of aquatic ecosystems that will support and enhance the lives of urban residents. One ecosystem cannot provide all of the necessary ecosystem services, thus we propose the use of ecosystem “flowers,” after Foley et al. (2005), which show the magnitude of ecosystem services depicted on multiple axes. These flowers can be used for both assessment of existing ecosystems and planning ecosystem design. Planners and managers could conduct a regional assessment of existing aquatic systems, evaluating the magnitude of services along each of the axes, or could create individual flowers for each ecosystem of interest. This exercise may reveal specific services that may be under-provided, thereby guiding future planning and design. Water in arid-land cities is a limiting resource at many levels; coordinated ecosystem design (as opposed to “restoration”) may actually allow the creation of aquatic systems that are multi-purpose and sustainable from the perspective of water managers, city planners and ecologists alike.