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Motility is important for bacteria for their survival, adaptation, and pathogenesis, especially in complex environments such as mucus, tissues, and biofilms. Although bacterial motility has been extensively studied based on imaging and tracking bacterial cell bodies, how the behavior and dynamics of the flagellar filaments of bacteria are affected by complex environments remains largely unexplored. To address this knowledge gap, we exploited site-directed mutagenesis and specific fluorescence labeling and directly visualized the flagellar filaments of Escherichia coli (E. coli) bacteria in polyethylene glycol-based hydrogel under fluorescence microscopy. We observed and classified three distinct types of flagellar motions of the E. coli bacteria in hydrogels: swimming (SWIM), trapped (TRAP), and stalled (STALL). Additionally, we quantified and compared the shapes and behaviors of the bacterial flagella of the three types using various shape quantifiers and descriptors. We found that these shape descriptors and quantifiers reliably and consistently reported the behaviors of the bacterial flagellar filaments. We examined the correlation of bacterial motility and flagellar dynamics for the three types, and found that the interactions of the bacterial flagella and hydrogel polymers/mesh reduced such correlation. Last, we inspected the flagellar filaments in more detail and identified their abnormalities due to hydrogel confinement and entanglement of the flagellar filaments with hydrogel polymers. The methods and analyses from this study are expected to support future efforts to develop and optimize hydrogels for more effective trapping of motile bacteria, thereby informing improved contamination-control strategies in hydrogel-related biomedical applications.