There is equivocal evidence regarding the benefits of aquatic aerobic exercise for non-specific chronic low back pain (NSCLBP) in addition to standard care in general practice consisting of education and advice. The purpose of this study was to compare the addition of deep water running (DWR) to standard general practice (GP) on NSCLBP versus GP care alone on pain, physical and mental health and disability. In this single-blind randomised controlled trial, 58 subjects with NSCLBP were recruited from primary care. The control group received GP care consisting of a physician’s consultation and educational booklet only. The experimental group received additional 30-min sessions of DWR three times a week for 15 weeks at the individualized aerobic threshold. Measurements were made pre- and post-intervention and at 1-year follow-up. Both groups showed improvement. The difference between treatment effects at longest follow-up of 1 year was −26.0 (−40.9 to −11.1) mm on the VAS (p < 0.05), −2.5 (−5.7 to −0.2) points in RMQ for disability (p < 0.05), 3.3 (10.0 to 24.7) points on physical health in the physical summary component of the Spanish Short Form 12 (SF-12; p < 0.05) and 5.8 (8.6 to 34.7) points on the mental summary component of the SF-12 (p < 0.05), in favour of the DWR group. For patients with NSCLBP, the addition of DWR to GP was more effective in reducing pain and disability than standard GP alone, suggesting the effectiveness and acceptability of this approach with this group of patients.