The commercialization of biofuels produced from microalgae is in its very early stages, and many resource-management practices and processes along the supply chain are still flexible. Guidance can ensure that the supply chain is as environmentally sustainable as possible. Better management practices (BMPs) for water quality and quantity, biodiversity, and greenhouse gas emissions are being developed in concert with studies of economic feasibility and algal productivity. Some BMPs are intended to meet numerical environmental targets, such as percent reductions in nutrient loadings to streams, whereas others are intended to avoid thresholds for adverse health or ecological effects. Still others are best available technologies developed iteratively through life-cycle and techno-economic analyses, which represent tradeoffs between profitability and environmental sustainability. As with forestry and agriculture, many BMPs for microalgae cultivation focus on water quality and quantity. But unlike BMPs for most agriculture and forestry applications, some proposed BMPs for algae biomass production reflect the regulatory emphasis on improving GHG emissions to obtain advanced biofuel designation. These BMPs are meant to characterize the state of science and engineering, rather than to represent hurdles or requirements.