Ecological modeling of dynamic systems such as marine environments may require detailed spatial resolution when the modeled area is greatly influenced by complex physical circulation. Therefore, the simulation of a marine ecosystem must be underlain by a physical model. However, coupling hydrodynamic and biogeochemical models is not straightforward. This paper presents a modeling technique that can be used to build generic and flexible fully-spatial physical-biogeochemical models to study coastal marine ecosystems using a visual modeling environment (VME). The model core is constructed in Simile, a VME that has the capacity to create multiple instances of submodels that can be interconnected, producing a fully-spatial simulation. The core is designed to assimilate a choice of different hydrodynamic models by means of matrices, enhancing its compatibility with different software. The biogeochemical model can be modified by means of a graphical interface, which facilitates sharing within the scientific community. This paper demonstrates the application of the coupling scheme to mussel aquaculture in Tracadie Bay (PEI, Eastern Canada). The model was run for two different years, 1998 and 1999, and indicated that mussel biomass exerts a top-down control of phytoplankton populations, causing a maximum chlorophyll depletion of 61.0% and 80.3% for 1998 and 1999 respectively. The difference between both years highlights the importance of inter-annual variability, which is significant from an ecosystem-level perspective because it reveals the relevance of applying a precautionary policy in the management of aquaculture activity. Therefore, the proposed core developed in Simile is a generic and flexible tool for modeling long-term processes in coastal waters, which is able to assimilate a choice of hydrodynamic models, constituting a novel approach for generating fully-spatial models using visual modeling environments. (C) 2011 Elsevier B.V. All rights reserved.