Increasing demands for agricultural water require identification of alternative water sources. Enterococcus species can exhibit antimicrobial resistance and transfer resistance traits to other bacterial taxa, including human pathogens. This study evaluated the distribution and antimicrobial resistance of Enterococcus faecalis and E. faecium in surface and recycled waters. In all, 365 isolates from 129 water samples collected over one year were identified by species, and 95 were selected for antimicrobial susceptibility testing. Season, water type, temperature and salinity were statistically significantly associated with species probability, and season with antimicrobial resistance of E. faecalis. 1.3% of E. faecalis and 5.0% E. faecium were pan-susceptible but 100% were susceptible to ampicillin, vancomycin, daptomycin and linezolid. Multidrug resistance was detected in 16% of E. faecalis and 70% of E. faecium isolates. Enterococcus was ubiquitous in water and exhibited resistance to multiple antimicrobials, but resistance to antimicrobials of last resort for enterococcal infections was non-existent.