The present paper focuses on demonstrating the capabilities of modern hydroinformatics tools in the field of environmental systems by integrating biotic and abiotic process modelling. Abiotic processes like hydrodynamic flow and transport phenomena are often formulated based on physical principles like conservation of mass, momentum and energy. These processes are adequately represented mathematically by second order partial differential equations that can be solved numerically in a variety of ways. However, in aquatic ecosystem modelling, biological/ecological processes play an important role and these processes are not always understood at the required level of detail to be captured in terms of conservation principles. In this paper two modelling approaches for biotic processes are explored for representing spatial pattern dynamics of aquatic ecosystems: (i) cellular automata (CA) and (ii) multi-agent systems (MAS) models, in combination with Delft 3D-WAQ for advanced flow and transport modelling. It is shown that CA are quite capable of capturing discrete growth phenomena like outcompeting plant species which are known to depend mainly on local effects. A MAS approach can combine nonlinearity, randomness and complexity of aquatic ecosystems, which can then be used to enhance the capabilities of available physics-based software systems like the DELFT3D software suite.