<p>The large-scale production of biogas slurry, a by-product of anaerobic digestion, presents significant opportunities for reuse sustainable in agricultural. Subsurface drip irrigation (SDI) offers a precise and controlled method for biogas slurry application. However, emitter clogging remains a major challenge, attributed to high concentrations of microorganisms and suspended solids in biogas slurry. This study conducted a 720-hour in-situ field-scale accelerated experiment to investigate clogging mechanisms in groundwater (CK) and biogas slurry (BS) irrigation systems. Confocal laser scanning microscopy (CLSM), X-ray diffraction (XRD), and 16&#xa0;S rRNA sequencing were employed to characterize the clogging substance (CS). The results showed significant increases in bacterial gene copy numbers (66.08–136.88%) and extracellular polymeric substances (EPS) contents (31.15–68.20%) during the middle and end stages of the experiment. Significant disparities were observed in bacterial community composition: CK exhibited larger and more complex molecular ecological networks (MENs), whereas BS treatments displayed higher connectivity (11.181 vs. 9.573), modularity (0.879 vs. 0.800), and network stability. Random forest (RF) analysis identified quartz as the most important variable, contributing 32.37–51.01% to the dominant composition of clogging substances. Water quality factors, including COD_cr and TSS, showed significant correlations with mineral precipitations dynamics, while BOD₅ and TSS notably influenced key modules of MENs. This study establishes a foundation for developing water quality control standards and provides insights for optimizing wastewater treatment and filtration equipment to mitigate emitter clogging, thereby improving the performance and longevity of SDI systems utilizing biogas slurry.</p>