For quantitative modelling, our default modelling tools include, but are not limited to, the following.
QGIS for geographical information and analysis
Ecopath with Ecosim and Ecospace for ecological/ecosystem modelling
Ecolego for contaminant transport and environmental risk assessment modelling and sensitivity/uncertainty analyses
ERICA Assessment Tool for assessing radiological risk to biota
GNU Octave for the more demanding data processing and numerical modelling