Abstract Background Worldwide, studies show a relationship between nurses’ health and some work environment factors; however, data on nurses’ health and self-perceived workload and nursing task allocation are lacking, particularly for Lebanese nurses. We assessed the relationship of several work environment factors: overall workload and specific temporal, physical, mental, effort, frustration, and performance demands (NASA Task Load Index), staffing resources and adequacy and leadership (Practice Environment Scale of Nursing Work Index), teamwork climate (Safety Attitudes Questionnaire), and nursing task allocation (Basel Extent of Rationing of Nursing Care)) with self-reported musculoskeletal, cardiovascular, skin, and mental health diseases (Work Ability Index) and emotional exhaustion (Maslach Burnout Inventory) among Lebanese nurses. Methods A cross-sectional self-report survey was distributed to all 289 registered nurses (RNs) in the medical, surgical, and pediatric units in two Lebanese university-affiliated hospitals; 170 RNs had complete data. Adjusted multivariable logistic regression models were used to estimate the association between work environment factors and health outcomes. Results The most prevalent outcomes were musculoskeletal disease (69%), emotional exhaustion (59%), and mental health problems (56%); 70% of RNs had ≥2 and 35.29% had ≥4 co-occurring health problems. Musculoskeletal disease was associated with higher overall (OR = 1.36 (95%CI = 1.03, 1.80)), temporal (OR = 1.30 (95%CI = 1.09, 1.55)), and physical demands (OR = 1.20 (95%CI = 1.03, 1.49)), higher task allocation to RNs (OR = 1.11 (95%CI = 1.01, 1.23)) and lower teamwork climate (OR = 0.60 (95%CI = 0.36, 0.98). Higher odds of mental/emotional problems were associated with higher overall, temporal, frustration, and effort demands, and lower teamwork climate, performance satisfaction, and resources adequacy (increased odds ranging from 18 to 88%). Work environment indicators were associated with higher co-occurrence of health problems. Conclusions Results show elevated health burden and co-morbidity among Lebanese RNs and highlight the value of comprehensive approaches that can simultaneously improve several work environment factors (namely self-perceived workload, teamwork,, resources, and nursing task allocation) to reduce this burden.