Fractured aquifers are heterogeneous due to the variable frequency, orientation, and intersections of rock discontinuities. A ~100-m-thick Silurian dolostone sequence provides a bedrock aquifer supplying the city of Guelph, Canada. Here, fracture network characteristics and associated influences on hydraulic head were examined using several data types obtained from 24 cored holes in a study that is novel for the quantity and quality of data. High (50–90°) angle joint orientations, heights, and terminations relative to bedding features were determined from acoustic televiewer logs and outcrop scanlines. These data were compared to high-resolution hydraulic head profiles showing head loss over depth-discrete intervals identifying zones with lower vertical hydraulic conductivity. This study reveals that the marl-rich Vinemount Member, traditionally considered the principal aquitard, corresponds to head loss in only 62% of the 24 boreholes. The vertical position of head loss varies across the 90-km2 study area and occurs in any of the lithostratigraphic units of the Lockport Group. Within this sedimentary sequence, aquitards are laterally discontinuous or “patchy” at variable depths and relate to: (1) the frequency of the high-angle joints; (2) shorter joint height; and (3) the type of joint terminations. The head loss occurs in thin (2–2.5 m) intervals where the frequency of the high-angle joints is low. Where a large proportion of small joints cross-cut marl bedding planes, head loss is negligible, suggesting that the vertical hydraulic conductivity is not reduced. Overall, these findings are potentially applicable to assessing aquitard and cap rock integrity in carbonate sedimentary sequences worldwide.