The long-term aim of this work is to develop a biosensing system that rapidly detects bacterial targets of interest, such as Escherichia coli, in drinking and recreational water quality monitoring. For these applications, a standard sample size is 100 mL, which is quite large for magnetic separation microfluidic analysis platforms that typically function with <20 µL/s throughput. Here, we report the use of 1.5-µm-diameter magnetic microdisc to selectively tag target bacteria, and a high-throughput microfluidic device that can potentially isolate the magnetically tagged bacteria from 100 mL water samples in less than 15 min. Simulations and experiments show~90% capture efficiencies of magnetic particles at flow rates up to 120 µL/s. Also, the platform enables the magnetic microdiscs/bacteria conjugates to be directly imaged, providing a path for quantitative assay.From the large-volume samples experiments with IONs, the magnetic separation microfluidic device was capable of processing > 50 mL samples (Figure 7). The 50 mL sample (IONs concentration of 100 µg/mL) was filtered in~7 min at a flow rate of 120 µL/s and the estimated capture efficiency was 70.0 ± 2.3%. Similarly, the 100 mL sample (IONs concentration 12.5 µg/mL, 100 mL) was filtered in Micromachines 2020, 11, 16 9 of 13 15 min at a flow rate of 120 µL/s and the estimated capture efficiency was 72.2 ± 2.0%. Figure 7 show 100 mL sample experiment images of the solutions before filtering (A), after filtering (B), the µFMS device with all captured IONs (C), and the VSM data to estimate capture efficiency for 100 mL sample (D).