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We present a methodology to model water, heat, and dissolved oxygen budgets on short time scales within a shallow estuarine environment using limited local water quality and climatic data. A tidally restricted eutrophic pond in Elkhorn Slough, California, experiences extreme diel dissolved oxygen (DO) variations during warm sunny days and neap tidal cycles. Empirical relationships between biological metabolism (measured as DO variations) and physical parameters are derived using time-series hydrographic data from the site. A simple box model predicts the time-series structure of water depth, water temperature, and DO concentrations within the pond as a function of the tidal cycle and local climate over 10 to 15 d simulation periods. Parametric analyses illustrate applications of the model to predict thermal and geochemical responses to hydrologic, chemical, and climatic alterations to the system. This study also initiates preliminary investigations of the fundamental processes influencing DO dynamics within a natural wetland environment, and could be used to explore the potential response to various physical and chemical alterations prior to restoration or management adjustments. Future box models of wetland geochemistry should include carbon and nutrient budgets to create a more sensitive model, and to allow more rigorous evaluations of the role decreased nutrient inputs would play in alleviating eutrophic conditions. KEY WORDS: Estuary · Wetland restoration model · Diel ecosystem metabolism · EutrophicationResale or republication not permitted without written consent of the publisher