Deep tubewells are a key component of arsenic mitigation programs in rural Bangladesh. Compared to widely prevalent shallow tubewells, deep tubewells reduce ground-water arsenic exposure and provide better microbial water quality at source. However, the benefits of clean drinking-water at these more distant sources may be abated by higher levels of microbial contamination at point-of-use. One such potential pathway is the use of contaminated surface water for washing drinking-water storage containers. The aim of this study is to compare the prevalence of surface water use for washing drinking-water storage containers among deep and shallow tubewell users in a cohort of 499 rural residents in Matlab, Bangladesh. We employ a multi-level logistic regression model to measure the effect of tubewell type and ownership status on the odds of washing storage containers with surface water. Results show that deep tubewell users who do not own their drinking-water tubewell, have 6.53 times the odds [95% CI: 3.56, 12.00] of using surface water for cleaning storage containers compared to shallow tubewell users, who own their drinking-water source. Even deep tubewell users who own a private well within walking distance have 2.53 [95% CI: 1.36, 4.71] times the odds of using surface water compared to their shallow tubewell counterparts. These results highlight the need for interventions to limit risk substitution, particularly the increased use of contaminated surface water when access to drinking water is reduced. Increasing ownership of and proximity to deep tubewells, although crucial, is insufficient to achieve equity in safe drinking-water access across rural Bangladesh.