Accurately assessing the microbiological safety of water sources is essential to reduce waterbornefecal exposures and track progress toward global targets of safe water access. Sanitary inspections are arecommended tool to assess water safety. We collected 1,684 water samples from 902 shallow tubewells in ruralBangladesh and conducted sanitary surveys to assess whether sanitary risk scores could predict water quality, asmeasured byEscherichia coli. We detectedE.coliin 41% of tubewells, mostly at low concentrations. Based on sani-tary scores, 31% of wells were low risk, 45% medium risk, and 25% high or very high risk. Older wells had higherrisk scores.Escherichia colilevels were higher in wells where the platform was cracked or broken (Δlog10= 0.09,0.00–0.18) or undercut by erosion (Δlog10= 0.13, 0.01–0.24). However, the positive predictive value of these risk fac-tors forE.colipresence was low (< 50%). Latrine presence within 10 m was not associated with water quality duringthe wet season but was associated with less frequentE.colidetection during the dry season (relative risk = 0.72,0.59–0.88). Sanitary scores were not associated withE.colipresence or concentration. These findings indicate thatobserved characteristics of a tubewell, as measured by sanitary inspections in their current form, do not sufficientlycharacterize microbiological water quality, as measured byE.coli. Assessments of local groundwater and geologicalconditions and improved water quality indicators may reveal more clear relationships. Our findings also suggest thatthe dominant contamination route for shallow groundwater sources is short-circuiting at the wellhead rather thansubsurface transport.