Increasingly, undergraduate institutions are incorporating original research into the curriculum as a matter of best practice. However, while the practice of science has grown more collaborative, undergraduate research has remained largely confined to single-institution studies. Incorporating long-term, distributed research projects into the undergraduate research experience can better prepare students to interpret and engage in science of the future. The Decomposition in Aquatic and Terrestrial Invaded Systems (DATIS) project within the Ecological Research as Education Network (EREN) offers a good model for examining how to minimize challenges and maximize opportunities associated with classroom use of long-term, collaborative research projects. Eleven key challenges are identified, and practical solutions are provided for each. By modeling this scientific approach in primarily undergraduate institutions, we are preparing graduates who will have the tools and knowledge to work collaboratively and create their own distributed research networks. Our goal is that the decomposition project we describe here can inform and inspire others seeking to engage in research at the undergraduate level, either as potential research coordinators or as collaborators in an existing network.