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Small scale marine environments (bays, channels, estuaries, marinas, etc.) are dynamic environments where diverse flora and fauna come into close contact with man-made processes. Yet water temperature monitoring of these coastal environments is usually spatially sparse due to the cost of acquiring, deploying and maintaining buoys. In this paper we introduce micro tomography: using precise time-of-flight calculations for acoustic signals sent over short distances (50 m) to measure water temperature. The traditional use of the technology is to construct low resolution temperature and current maps of large bodies of water useful for global climate study, however here we apply the key concepts to a sensor network to enable real-time monitoring of water temperature while also improving the spatial resolution of the data. As we use time-of-flight measurements to accomplish our goal, high precision and tight time synchronization are required of the network in order to produce meaningful temperature maps. On the other hand, the reduced scale introduces a new opportunity to utilize the technology to sense even the slightest change in temperature. To show our system is realizable we present our prototype underwater acoustic sensor nodes and experimental results that indicates a temperature resolution of approximately one-tenth of a degree Celsius. We also present our micro-tomography simulation software. With the simulator we can study the feasibility of building a more complex marina-scale tomography system and the requirements that must be met by the underlying sensor network.