Biodiversity decline and climate change are among the most important environmental issues society faces. Information to address these issues has benefited from increasing big data, advances in cloud computing, and subsequent new tools for analytics. Accessing such tools is streamlined by virtual laboratories for ecological analysis, like the ‘Biodiversity and Climate Change Virtual Laboratory’ (BCCVL) and ‘ecocloud’. These platforms help reduce time and effort spent on developing programming skills, data acquisition and curation, plus model building. Recently this functionality was extended, producing EcoCommons Australia—a web-based ecological modeling platform for environmental problem-solving—with upgraded infrastructure and improved ensemble modeling, post-model analysis, workflow transparency and reproducibility. We outline our user-centered approach to systems design, from initial surveys of stakeholder needs to user involvement in testing, and collaboration with specialists. We illustrate EcoCommons and compare model evaluation statistics through four cases studies, highlighting how the modular platform meets users’ needs.