This paper reports the first application of iterative experimental design methodology for high spatiotemporal resolution characterization of river and lake aquatic systems performed using mobile robot sensing systems. Both applications involve dynamic phenomena spread over large spatial domain: 1) Characterization of contaminant concentration and flow at the confluence of two major rivers displaying dynamics due to flow of the water; and 2) Characterization of rapidly evolving biological processes such as phytoplankton dynamics in a lake system. We describe the development and application of a new general purpose method for mobile robot sensing in such environments - Iterative experiment Design for Environmental Applications (IDEA). IDEA introduces in-field adaptation of mobile robotic sensing system. Analysis of the complex spatial and temporal structures associated with each observed environment is presented. Detailed characterization of the observed environment using IDEA methodology is used as an informed prior to improve the performance of the existing adaptive experimental design approaches for mobile robotic systems - stratified adaptive sampling and hierarchical non-stationary Gaussian Processes.