Julia Wondolleck has spent over 20 years researching the emergence and functioning of inter-organizational and community-based collaborative processes in ecosystem-scale resource management, processes that often arise in response to natural and/or social system crises. Her research focus is environmental decision-making and the structure of policy and administrative processes that promote the sustainability of ecological and human systems in the face of diverse yet legitimate interests, scientific complexity, and often conflicting and ambiguous legal direction. This research looks at both conflict and collaboration in the management of public natural resources and, in particular, the factors that promote and sustain community-based collaborative resource management processes. Current research projects include: assessing lessons for policy and practice from marine ecosystem-based management initiatives around the world; examining the experiences of Bureau of Land Management Resource Advisory Councils and NOAA National Marine Sanctuary Advisory Councils; determining the influence of the Federal Advisory Committee Act in public resource management; and, assessing approaches to evaluating the effectiveness of ecosystem-based management processes. Wondolleck is also examining the connections between what encourages and sustains collaborative ecosystem management initiatives and the institutional arrangements that might enable community-level adaptation to the effects of climate change.

Wondolleck's courses are largely case-based and discussion-oriented, and examine different dimensions of environmental decision-making in organizations, agencies and society in the face of conflict. She regularly teaches: NRE 532 (Natural Resource and Environmental Conflict Management); NRE 533 (Negotiation Skills in Environmental Dispute Resolution); and NRE 536 (Mediation Skills). She was awarded the Students for SNRE Outstanding Teaching Award three times, in 2010, 2003 and 2001.