Stromatolites are biogenic sedimentary structures formed by the interplay of biological (microbial composition) and environmental factors (local hydrodynamic conditions, clastic input and/or water chemistry). Well-preserved, three-dimensional (3D) fossil stromatolites are key to assessing the environmental factors controlling their growth and resulting morphology in space and time. Here, we report the detailed analysis of well-exposed, highly informative stromatolite build-ups from a single stratigraphic horizon within the Maastrichtian–Danian Yacoraite Formation (Argentina). This study focuses on the analysis of depositional processes driving intertidal to shallow subtidal stromatolites. Overall depositional architecture, external morphology and internal arrangement (mega, macro, meso and microstructures) of stromatolite build-ups were analysed and combined with 3D photogrammetric models, allowing us to decipher the links between stromatolite structure and tidal dynamics. Results suggest that external morphology and architecture of elongated and parallel clusters grew under the influence of run-off channels. The internal morphology exhibits columnar structures where the space between columns is interpreted as recharge or discharge channels. This work supports the theory that stromatolites can be used as a high-resolution tool in the assessment of water dynamics, and provides a new methodological approach and data for the dynamic reconstruction of intertidal stromatolite systems through the geological record.