In order to support environmental scientists in finding an «adequate» model of the system they are investigating, a computer program is necessary, which allows its users to perform simulations using different models, to assess the identifiability and to estimate the values of model parameters (using measured data), and to estimate prediction uncertainty. The computer program AQUASIM was developed to perform such analyses for technical and natural aquatic systems. AQUASIM allows its users to define the spatial configuration of the system to be investigated as a set of compartments, which can be connected to each other by links. Currently, the available compartment types include mixed reactors, biofilm reactors (consisting of a biofilm and a bulk fluid phase), advective-diffusive reactors (plug flow reactors with or without dispersion), saturated soil columns (with sorption and pore volume exchange), river sections (describing water flow and substance transport and transformation in open channels) and lakes (describing stratification and substance transport and transformation in the water column of the lake and in adjacent sediment layers). Compartments can be connected by two types of links (lakes can not be linked to other compartments yet). Advective links represent water flow and advective substance transport between compartments, including bifurcations and junctions. Diffusive links represent boundary layers or membranes, which can be penetrated selectively by certain substances. The user of the program is free in specifying any set of state variables and transformation processes to be active within the compartments. For the model as defined by the user, the program is able to perform simulations, sensitivity analyses and parameter estimations using measured data. These features make the program a very useful research tool. Calculated results can be plotted to the screen (window interface version only), written to a Post-Script file for transfer to a printer...