Corpus Christi Bay (TX, USA) is a shallow wind-driven bay and thereby, can be characterized as a highly pulsed system. It cycles through various episodic events such as hypoxia, water column stratification, sediment resuspension, flooding, etc. Understanding of the processes that control these events requires an efficient observation system that can measure various hydrodynamic and water quality parameters at the multitude of spatial and temporal scales of interest. As part of our effort to implement an efficient observation system for Corpus Christi Bay, a mobile monitoring system was developed that can acquire and visualize data measured by various submersible sensors on an undulating tow-body deployed behind a research vessel. Along with this system, we have installed a downward-looking Acoustic Doppler Current Profiler to measure the vertical profile of water currents. Real-time display of each measured parameter intensity (measured value relative to a pre-set peak value) guides in selecting the transect route to capture the event of interest. In addition, large synchronized datasets measured by this system provide an opportunity to understand the processes that control various episodic events in the bay. To illustrate the capability of this system, datasets from two research cruises are presented in this paper that help to clarify processes inducing an inverse estuary condition at the mouth of the ship channel and hypoxia at the bottom of the bay. These measured datasets can also be used to drive numerical models to understand various environmental phenomena that control the water quality of the bay.