Well clogging was studied at an aquifer storage transfer and recovery (ASTR) site used to secure freshwater supply for a flower bulb farm. Tile drainage water (TDW) was collected from a 10-ha parcel, stored in a sandy brackish coastal aquifer via well injection in wet periods, and reused during dry periods. This ASTR application has been susceptible to clogging, as the TDW composition largely exceeded most clogging mitigation guidelines. TDW pretreatment by sand filtration did not cause substantial clogging at a smaller ASR site (2 ha) at the same farm. In the current (10 ha) system, sand filtration was substituted by 40-μm disc filters to lower costs (by 10,000–30,000 Euro) and reduce space (by 50–100 m2). This measure treated TDW insufficiently and injection wells rapidly clogged. Chemical, biological, and physical clogging occurred, as observed from elemental, organic carbon, 16S rRNA, and grain-size distribution analyses of the clogging material. Physical clogging by particles was the main cause, based on the strong relation between injected turbidity load and normalized well injectivity. Periodical backflushing of injection wells improved operation, although the disc filters clogged when the turbidity increased (up to 165 NTU) during a severe rainfall event (44 mm in 3 days). Automated periodical backflushing, together with regulating the maximum turbidity (<20 NTU) of the TDW, protected ASTR operation, but reduced the injected TDW volume by ~20–25%. The studied clogging-prevention measures collectively are only viable as an alternative for sand filtration when the injected volume remains sufficient to secure the farmer’s needs for irrigation.