Small-scale marine environments (bays, marinas, etc.) are dynamic environments where diverse flora and fauna come into close contact with man-made processes. Yet, water temperature monitoring of coastal environments is spatially sparse due to the cost of acquiring, deploying and maintaining buoys. Here we introduce microtomography: using precise time-of-flight calculations for acoustic signals sent over short distances to measure water temperature. Traditionally, tomography is used at ocean scale, 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. We present our prototype underwater acoustic sensor nodes and experimental results that indicate a temperature resolution of approximately one-tenth of a degree Celsius. We also present our microtomography simulation software that allows us to study the feasibility of building complex marina-scale tomography systems and the requirements that must be met by the underlying sensor network.