The present study aimed to investigate the potential application of chitosan (CS) and its two derivatives, dialdehyde chitosan (DCT) and carboxymethyl chitosan (CMC), as new flocculants in the purification of filter backwash water. The main objective of the work was to remove the disadvantages and inconveniences associated with using synthetic flocculants, mainly based on polyacrylamide, by using biodegradable and non-toxic biopolymer flocculants. The chitosan derivatives were obtained in the process of the chemical modification of this polysaccharide. CS was oxidated with periodate in acetic acid solution to obtain DCT with a degree of substitution (DS) of 44.29%. For the CMC synthesis, after the alkaline activation of chitosan, the solution was treated with monochloroacetic acid (MCA) at 60 °C for 3 h, leading to carboxymethylated chitosan formation with a DS of 49.55%. Characterizations of the flocculants using Fourier transform infrared (FT-IR) spectroscopy, 13C nuclear magnetic resonance (13C NMR) spectroscopy, and an elementary analysis confirmed the successful modification of the chitosan. The morphology and thermal stability of the samples were investigated using scanning electron microscopy (SEM) and a thermogravimetric analysis (TGA), respectively. Moreover, the biopolymer materials were studied in a series of flocculation jar tests for filter backwash water samples collected at a water treatment plant (WTP) in Kutno, Poland. CMC turned out to be a particularly effective agent in an optimal amount of 0.2 mg/L, achieving nearly 99% iron removal and 98.26% turbidity removal efficiency rates, which indicates that chitosan–based materials can be ecological alternatives for polyacrylamide flocculants, effectively removing the impurities of iron ions.