Microalgae are promising natural resources for biofuels, chemical, food and feed products. Besides their economic potential, the environmental sustainability must be examined. Cultivation has a significant environmental impact that depends on reactor selection and operating conditions. To identify the main environmental bottlenecks for scale-up to industrial facilities this study provides a comparative life cycle assessment (LCA) of open raceway ponds and tubular photobioreactors at pilot scale. The results are based on experimental data from real pilot plants operated in summer, fall and winter at AIgaePARC (Wageningen, The Netherlands). The energy consumption for temperature regulation presented the highest environmental burden. The production of nutrients affected some categories. Despite limited differences compared to the vertical system, the horizontal PBR was found the most efficient in terms of productivity and environmental impact. The ORP was, given the Dutch climatic conditions, only feasible under summer operation. The results highlight the relevance of LCA as a tool for decision-making in process design. Weather conditions and availability of sources for temperature regulation were identified as essential factors for the selection of geographic locations and for microalgal cultivation systems based on environmental criteria. Simulation of large-scale reactors with optimized temperature regulation systems lead to environmental improvements and energy demand reductions ranging from 17% up to 90% for systems operated in favorable summer conditions.