The commercialization of biofuels produced from microalgae is in its infancy; therefore, many resource-management practices and production processes are still flexible. The purpose of this paper is to guide development of supply chains toward more environmentally sustainable practices. We review current and projected technologies and practices for autotrophic microalgae cultivation that promote environmental sustainability. We develop a framework that leverages these studies to propose better management practices (BMPs) for water quality and quantity, biodiversity, or greenhouse gas emissions in concert with productivity and profitability considerations. Some proposed BMPs are linked to numerical environmental targets, such as percent reductions in nutrient loadings to streams, whereas others seek to avoid thresholds leading to adverse health or ecological effects. Still others involve using the best available technologies, developed iteratively through life-cycle and techno-economic analyses. Proposed BMPs for microalgae cultivation focus on water quality and quantity, as well as improving greenhouse gas (GHG) emissions to obtain advanced biofuel designation. BMPs must allow producers to meet productivity and profitability targets, as well as environmental targets. These example BMPs characterize the state of science and engineering; thus, they will change over time.