During the several last decades, environmental scientists use numerical modeling as a tool in their studies and investigations of aquatic systems. Ecological and hydrodynamic models are developed in parallel regarding their complexity, uncertainty, and computational power. Ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, evaluate remedial practices in response to eutrophication etc. This review paper deals with the progress in ecological modeling related to eutrophication processes, specifically in models that describe the trophic state dynamics of hypoxic/anoxic aquatic ecosystems. Nine dynamic ecological models coupled or noncoupled with hydrodynamic models have been discussed based upon their history, complexity, limitations, recent detailed modeling applications, and their important results. The advantages and disadvantages of these models are presented along with their application areas.