Quoted from: https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.471.7532&rep=rep1&type=pdf 

CAEDYM is an aquatic ecological model designed to be readily linked to hydrodynamic models, which currently includes DYRESM, DYRIM and ELCOM. DYRESM is a one-dimensional model used for predicting vertical density stratification in lakes and reservoirs (Gal et al., 2003; Yeates and Imberger, 2004). It has been coupled previously with process representations of biogeochemical processes (DYRESM-WQ: Hamilton and Schladow (1997); Schladow and Hamilton (1997); Hamilton et al. (1995); Schladow and Hamilton (1995)). ELCOM is a three-dimensional hydrodynamic model applicable to lakes (Hodges et al., 2000), reservoirs (Romero and Imberger, 2003; Romero et al., 2003), estuaries (Robson and Hamilton, 2004; Chan et al., 2002) and the coastal ocean (Spillman et al., 2005; Hillmer and Imberger, 2005). Recently, CAEDYM has been coupled to DYRIM (a quasi-2D Lagrangian riverfloodplain model; Devkota and Imberger (2005)) to simulate biogeochemical processing in rivers. The coupling between CAEDYM and the hydrodynamic driver is dynamic; in particular, the thermal structure of the water body is dependent on the water quality concentrations by feeding back through water clarity.

      One of the objectives during CAEDYM development was to allow flexible ecological configuration that could be tailored for specific applications, though major elemental cycling and at least one algal group is compulsory. Hence, the model includes comprehensive process representation of the C, N, P, Si and DO cycles, several size classes of inorganic suspended solids, and phytoplankton dynamics. Numerous optional biological and other state variables can also be configured. Hence, CAEDYM is more advanced than traditional N-P-Z models, as it is a general biogeochemical model that can resolve species- or group-specific ecological interactions. CAEDYM operates on any sub-daily time step to resolve algal processes (diurnal photosynthesis and nocturnal respiration), and is generally run at the same time interval as the hydrodynamic model. Algorithms for salinity dependence are included so that a diverse range of aquatic settings can be simulated. The user can prescribe whether the simulation is for freshwater, estuaries or coastal waters, since many of the algorithms have been developed to include a salinity dependence. With specification of the nature of the waterbody (i.e. fresh, estuarine or marine), internal checks in the model are then activated to ensure that salinity dependence is maintained (for an estuarine case) or removed (for a freshwater or marine water case). Further details of salinity dependence are given later in the process descriptions.

      The major biogeochemical state variables in CAEDYM are given in Figure 1.1. A simple configuration file exists that allows users to customise the model elements that should be included within any simulation. An input file for parameters can also be adjusted rather than modifying the source code, but inevitably, a small number of users will have specific variables of interest which have not been represented in CAEDYM, thus necessitating some modification to the source code.