(1) Background: Water is necessary for the preparation of some medicines found in pharmacies where the local water source does not meet the required purity. This study aimed to investigate the presence of coliform contamination in water used for drug reconstitution in community pharmacies in Jordan. (2) Methods: Two water samples from 50 randomly selected community pharmacies representing all Jordanian governorates were filtered and then cultured in plate count agars to determine total microbial count, and in m-Endo Agar Les and Eosin Methylene Blue (EMB) agar to cultivate Escherichia coli (E. coli). The presence of E. coli was further characterized with gram stains, biochemical tests, and Polymerase chain reaction (PCR). Antibiotic susceptibility of isolated E. coli was tested against a variety of standard antibiotics. (3) Results: Community pharmacies used droppers filled with water from coolers (62%), bottled water (20%), boiled tap water (16%) and tap water (2%). The majority of the sampled water contained coliform bacteria (88%), and E. coli was isolated from 26% of all samples. Statistical analysis showed no significant difference in the percentage of contaminated water samples based on its source location. Nonetheless, the results showed a tendency for higher proportions of contamination in droppers filled from boiled tap water (37.5%; SE: 17.1), followed by water from water coolers (25.8%; SE: 7.9), and then from bottled water (20%; SE: 12.7). All of the isolated E. coli were sensitive to gentamycin, ciprofloxacin and levofloxacin. The susceptibility of the isolates to ceftazidime, doxycycline, tetracycline, azithromycin and amoxicillin/clavulanic acid were 92%, 61%, 46%, 23% and 15%, respectively. (4) Conclusions: This study confirms the widespread presence of multidrug-resistant bacteria in water intended for reconstituting drugs in local pharmacies. These findings expose an alarming situation that needs special attention by the acting pharmacists and competent authorities. Higher levels of personal hygiene in the pharmacies coupled with regular inspection of water quality may reduce the risk of microbial contamination in compounded products, especially multidrug-resistant strains of E. coli and other index microorganisms.