Low-cost platforms such as kites and balloons are an alternative means for collecting data over small areas and have been used for aerial photography, for example in agriculture, ecology and archaeology although typically are used to acquire a single or a small number of photographs. In this paper we develop data collection techniques and data processing algorithms for constructing ultra-high resolution (sub-centimeter) three-dimensional maps of intertidal rock platforms with a low-cost kite-based mapping system using hundreds of photographs over a broad area. A photogrammetric pipeline was developed for constructing high-resolution, three-dimensional, photo-realistic terrain models using multiple low-altitude images collected from a consumer-grade digital camera on-board the kite platform. The resulting maps combine color (potentially multispectral) and topographic information, thus enabling spatial properties of the intertidal environment to be determined across a hierarchy of spatial scales. Potential uses of this technique include mapping of plant (micro- and macro-algae) and animal (e.g. gastropods) assemblages at multiple spatial and temporal scales.