Background Web-based mindfulness interventions are increasingly delivered through the internet to treat mental health conditions. Objective The objective of this study was to determine the effectiveness of web-based mindfulness interventions in clinical mental health populations. Secondary aims were to explore the impact of study variables on the effectiveness of web-based mindfulness interventions. Methods We performed a systematic review and meta-analysis of studies investigating the effects of web-based mindfulness interventions on clinical populations. Results The search strategy yielded 12 eligible studies. Web-based mindfulness interventions were effective in reducing depression in the total clinical sample (n=656 g=−0.609, P=.004) and in the anxiety disorder subgroup (n=313, g=−0.651, P<.001), but not in the depression disorder subgroup (n=251, P=.18). Similarly, web-based mindfulness interventions significantly reduced anxiety in the total clinical sample (n=756, g=−0.433, P=.004) and the anxiety disorder subgroup (n=413, g=−0.719, P<.001), but not in the depression disorder group (n=251, g=−0.213, P=.28). Finally, web-based mindfulness interventions improved quality of life and functioning in the total sample (n=591, g=0.362, P=.02) in the anxiety disorder subgroup (n=370, g=0.550, P=.02) and mindfulness skills in the total clinical sample (n=251, g=0.724, P<.001). Conclusions Results support the effectiveness of web-based mindfulness interventions in reducing depression and anxiety and in enhancing quality of life and mindfulness skills, particularly in those with clinical anxiety. Results should be interpreted with caution given the high heterogeneity of web-based mindfulness interventions and the low number of studies included.