Physics and Ecology in Fluids: Modeling and Numerical Experiments develops mathematical and numerical modeling methodologies for coupled biological-hydrodynamic problems with a focus on process studies. The modeling is presented in a way that discusses mathematical background but does not depend on a large body of mathematical pre-requisites or experience. Models are built up from simple, to complex. This includes discussion of approximations and shortcuts commonly made by large computational models for natural bodies of water. Computational approaches are presented using conceptual explanations and pseudo-code along with well-documented, open-source code. Over a dozen codes that run locally on the reader's laptop provide hands on experience with various aspects of the modeling process and its scientific results. One large-scale code for basin scale modeling based on the Discontinuous Galerkin methodology is presented, along with a self-contained discussion of theoretical background and implementation details. Physics and Ecology in Fluids is written for graduate students, academic researchers and government scientists. Professors can use the book as a stand-alone resource for a one term graduate course, or to supplement teaching of their own graduate courses. All readers may also use the book as background/user's guide for the software included with the book.