Regulatory water quality limits are extended from the wastewater resource recovery facility (WRRF) to the sewer system. It is thus necessary to properly integrate those systems for the evaluation of the overall emissions to the receiving water. The integration of the sewer system and the WRRF, however, leaves us with multiple potential options to reduce these emissions. The proposed approach builds on previous research using global sensitivity analysis (GSA) as a screening method for available control handles. It considers parameter and input uncertainty to select control handles that generate large benefits even if the model differs from reality. Results from a real-life case study indicate that the three top-rated handles are comparably effective for all considered uncertainty and variability scenarios. But the results also showed that this does not apply to lower-rated handles.