Bioturbated carbonate rocks can form high-quality aquifers and reservoirs. Although the controls on the porosity and permeability of these rocks are fairly understood at the well-bore scale, how such characteristics vary spatially across various scales of observation is still a major unsolved problem. This study integrates results of outcrop observations, imaging with scanning electron microscopy (SEM), computer tomographic (CT) scanning, petrographic analysis, and petrophysical measurements to understand how burrow intensity and burrowing style control the spatial variability of porosity and permeability of one stratum accumulated in a carbonate ramp. The CT scan data revealed two burrowing styles, pipe framework (in the upper part of the stratum, surface constrained textural heterogeneity) and bio-retexturing (in the lower part of the stratum, non-surface-constrained textural heterogeneity). The studied stratum is dominated by the micropores (cross-section>10 μm) of the host rock matrix (HRM), which comprise >50 % of the total porosity within the stratum. Porosity in the stratum does not vary substantially in vertical or lateral trends. In contrast, and perhaps most importantly, permeability does vary vertically and laterally depending on the scale of measurement, burrow percentage, and burrowing style. These results suggested that the storage capacity of the studied stratum is independent of bioturbation, whereas the flow capacity is strongly dependent on bioturbation. There is a substantial vertical change in permeability in the stratum in comparison to only small changes in the lateral direction across the layer of interest. The data also suggested that the subtle lateral change in permeability is controlled by bio-retexturing, which resulted in the homogenization of grain-dominated and mud-dominated sediments by bioturbation. Such a process can be destructive for the permeability compared to the pipe-connected burrowing style. We clearly show that the ichnologically-controlled porosity and permeability trends of the studied stratum are relevant at the field scale. Understanding such trends in the context of paleoenvironmental conditions provides insight into the fluid flow quality of bioturbated carbonates, which constitute a large proportion of water aquifers and hydrocarbon reservoirs globally.