The purpose of applying ecological models to lakes is to improve their management and protection, and to predict future changes in the lake water environment. Although ecological models cannot necessarily incorporate all significant processes, they should integrate the biomass and metabolic characteristics of the dominant primary producers, as well as the key secondary producers which directly graze upon them. In deep water systems, phytoplankton dominates the primary production, and zooplankton represents the secondary producer level. The biomass and metabolism of these two components are often described as a function of environmental variables based on the previous studies elsewhere. However, in shallow water lakes and even the inshore areas of deeper lakes, benthic organisms such as filter-feeding bivalves can play an important role as grazers on the phytoplankton. This type of local, site-specific effect is essential to incorporate within whole-lake models. This additional component may complicate the model, although can sometimes lead to useful simplifications. The development of models for specific sites requires a clear formulation of the objectives, and the acquisition of appropriate, site-specific data. Field observations are therefore essential to guide the modeling effort, to identify critical, site-specific mechanisms and to obtain realistic estimates of the input parameters for the model.