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The main goal of this work is to provide an advanced visual environment where users that are not skilled for what concerns the computer science domain may compose queries related to those geographical phenomena for which the third dimension is a relevant feature. Visual queries are composed in a 3D environment accessible from the web where the users manipulate geographical objects, called 3D geometaphors. The geometaphors represent the operands of an underlying algebra characterized by a set of topological, directional and metrical operators; such operators are expressed in the query environment in terms of visual relationships between the geographical objects. The introduction of the third dimension for querying the geographical databases has challenged the authors with a number of important issues related to the area of visualization, navigation and object manipulation. According to the principles of usability engineering, the authors have built different prototypes based on a client-server architecture that have been iteratively evaluated by experts and final users in order to discover drawbacks and to improve the quality of the proposal. The result is a coordinated user-friendly 3D visual metaphor for querying GIS on the web, where all the elements needed for composing a query have a visual, easy to understand, counterpart.