Shale gas pipeline development can have negative environmental impacts, including adverse effects on species and ecosystems through habitat degradation and loss. From a societal perspective, pipeline development planning processes should account for such externalities. We develop a multi-objective binary integer-programming model, called the Multi Objective Pipeline Siting (MOPS) model, to incorporate habitat externalities into pipeline development and to estimate the tradeoffs between pipeline development costs and habitat impacts. We demonstrate the utility of the model using an application from Bradford and Susquehanna counties in northeastern Pennsylvania. We find that significant habitat impacts could be avoided for relatively low cost, but that avoiding additional habitat impacts becomes gradually and increasingly costly. For example, 10 percent of the habitat impacts can be avoided at less than a two percent pipeline cost increase relative to a configuration that ignores habitat impacts. MOPS or a similar model could be integrated into the pipeline siting and permitting process, so oil and gas companies, communities, and states can identify cost-effective options for habitat conservation near shale gas development.