This study addresses the critical aspects of injection well clogging as part of an Aquifer Storage, Transfer and Recovery (ASTR) pilot infiltrating tile drainage water (TDW) from agricultural field into an anoxic brackish sandy aquifer for later re-use as irrigation water for flower bulbs. Two ASTR injection periods suffering from clogging were intensely monitored during several weeks in 2019 to 2020. The wells were rehabilitated by methods of backflushing and mechanical cleaning (high-pressure jetting) and sampled to obtain information on the kind of clogging material. The recharge water is nutrient rich (PO4: 2-18 mgL-1, NO3: 6-50 mgL-1, NH4: 0.1-0.6 mgL-1, DOC: 25-32 mgL-1) and attained significantly turbid conditions (usually between 5-20 NTU; up to 160 NTU) caused by the removal of resuspended biochemical material in the tile drainage network by extreme precipitation and extensive drain discharge events. Consequentially, the 40 µm spin Klin-disc filters as pre-treatment step experienced reduced functionality due to clogging when subjected to high turbid loads. Microbial processes within the ASTR piping system additionally caused fluctuations in turbidity by periodic on/off operation, indicating a high potential for (bio)physical and biological clogging in the injection wells. Microscopic and (hydro)geochemical analysis of injectant and backflushed suspended solids demonstrated a significant contribution of injected Fe-hydroxyapatite flocs and biochemical material incorporating siliceous clay and silt particles below 40 µm, while pyrite and possibly calcite precipitants were flushed from the aquifer matrix when removing suspended matter from the wells. The injection of suspended material caused clogging predominantly by physical mechanisms. During standstill, the hydrochemical environment in the well indicated substantial microbial activity by reduced redox conditions in the well and the mobilization of Fe(II), Mn(II), P, and Ca, indicating the vulnerability for biological clogging. Improving the feasibility of the ASTR system requires the high clogging potential of TDW to be reduced. It is recommended to adopt a settling tank, rapid sand filtration followed by slow sand filtration as pre-treatment steps to reduce the physical and biological clogging potential. Various other recommendations to reduce the clogging risks are discussed further. Regarding the well rehabilitation, methods of compressed-air ‘jutteren’ are recommended to recovery the well performance by effectively removing residual clogging material from the gravelpack and borehole wall.