Science, engineering, and health-related laboratories in tertiary institutions generate liquid waste that may contain toxic heavy metals, including lead, cadmium, chromium, manganese, and iron. Poor segregation, treatment, handling, and disposal of laboratory waste may contaminate drains and nearby water sources. This study investigated the effects of laboratory waste disposal, effluent handling, and safety compliance practices on heavy metal contamination of water sources in selected tertiary institutions. A quantitative cross-sectional design was used, combining questionnaire data with laboratory analysis of water samples. Using multistage sampling and Cochran’s formula, 380 respondents were selected; however, 360 valid questionnaires were analysed. Ten water samples collected within or near laboratory complexes were analysed for lead, cadmium, chromium, manganese, and iron using Atomic Absorption Spectroscopy. Data were analysed using descriptive statistics, Pearson correlation, multiple regression, and ANOVA at the 0.05 significance level. Findings revealed a low overall level of laboratory waste-management practices (grand mean = 2.61), particularly in chemical waste segregation and effluent pre-treatment/neutralisation. Lead, cadmium, chromium, and iron exceeded WHO/NSDWQ guideline limits, while manganese remained within the permissible limit. Waste disposal, effluent handling, and safety compliance significantly predicted heavy metal contamination, jointly explaining 54.6% of the variation in the contamination index (R2=0.546R^2 = 0.546R2=0.546, p<0.05p < 0.05p<0.05). The study concludes that weak laboratory waste-management and effluent-control practices are significantly associated with elevated heavy metal contamination. It recommends improved waste segregation, effluent treatment facilities, routine water-quality monitoring, and regular safety training.