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Anaerobic digestion (AD) is a well-established waste-to-value technology commonly used at water resource recovery facilities (WRRFs), generating biogas from organic waste. However, the generated biogas is typically used only for heat and electricity generation due to contaminants, while the nutrient-rich AD effluent requires further treatment before environmental release. Methanotroph-microalgae cocultures have recently emerged as promising candidates for integrated biogas valorization and nutrient recovery. Although the choice of the coculture pairs is one of the most important factors that determine the performance of the application, there have not been any results on the comparison or screening of different coculture pairs for a desired application. To expedite the screening of methanotroph-microalgae cocultures for optimal performance, we developed a cost-effective screening system consisting of nine parallel bioreactors. The compact design of the system allows it to fit in a fume hood, and enables the simultaneous evaluation of multiple species with triplicates under uniformly controlled conditions. The system was applied to screen seven methanotrophs, five microalgae, and six methanotroph-microalgae coculture pairs on a diluted AD effluent from a local WRRF. To systematically assess the growth performance of different monocultures and cocultures, mathematical models that describe the microbial growth under batch cultivation were developed to determine the maximum growth rate, delay time, and carrying capacity from growth data, allowing for consistent and systematic assessment of different species, as well as the identification of the coculture pairs with synergistic and inhibitory interactions. The developed experimental system and modeling approach enabled expedited strain screening and unbiased assessment for integrated biogas valorization and nutrient recovery. Specifically, the cost of each bioreactor system in S3 is less than 5% of commercially available bioreactor system (such as Bioflo 120), while the screening throughput of S3 is 9 times that of a single bioreactor system. In addition, the identified synergistic cocultures demonstrate potential for scalable biogas valorization and nutrient recovery in wastewater treatment.