The continuous exposure of living organisms and microorganisms to antibiotics that have increasingly been found in various environmental compartments may be perilous. One group of antibacterial agents that have an environmental impact that has been very scarcely studied is nitrofuran derivatives. Their representative is nitrofurantoin (NFT)—a synthetic, broad-spectrum antibiotic that is often overdosed. The main aims of the study were to: (a) isolate and characterize new microbial strains that are able to grow in the presence of NFT, (b) investigate the ability of isolates to decompose NFT, and (c) study the impact of NFT on microbial cell properties. As a result, five microbial species were isolated. A 24-h contact of bacteria with NFT provoked modifications in microbial cell properties. The greatest differences were observed in Sphingobacterium thalpophilum P3d, in which a decrease in both total and inner membrane permeability (from 86.7% to 48.3% and from 0.49 to 0.42 µM min−1) as well as an increase in cell surface hydrophobicity (from 28.3% to 39.7%) were observed. Nitrofurantoin removal by selected microbial cultures ranged from 50% to 90% in 28 days, depending on the bacterial strain. Although the isolates were able to decompose the pharmaceutical, its presence significantly affected the bacterial cells. Hence, the environmental impact of NFT should be investigated to a greater extent.