Stromatolite shapes, sizes, and spacings are products of microbial processes and interactions with topography, sedimentation, and flow. Laboratory experiments and studies of modern microbial mats and sediments can help reconstruct processes that shaped some typical stromatolite forms and some atypical microbially influenced sediments from Neoproterozoic cap carbonates. Studies of modern, cohesive microbial mats indicate that microbialaminite facies in the lower Rasthof Formation (Cryogenian) formed in the presence of very low flow and were not deformed by strong waves or currents. Giant wave ripples, corrugated stromatolites, and tube-hosting stromatolites in basal Ediacaran cap carbonates record interactions between microbes, flow, and evolving bedforms. Preferential cementation in and close to the giant ripple crests is attributed to interactions between flow and local topography. These interactions pumped alkaline porewaters into ripple crests and helped nucleate elongated stromatolites. The similar textures of giant wave ripples and elongated, corrugated, and tube-hosting stromatolites suggest growth in the presence of organic-rich, rounded particles and microbial mats, and in flow regimes that permitted mat growth. These hypotheses can be tested by experiments and models that investigate lithification and the macroscopic morphology of microbial mats as a function of the flow regime, preexisting topography, redox-stratification in sediments, and delivery of organic-rich particles. The widespread microbially influenced textures in Cryogenian microbialaminites and basal Ediacaran cap dolostones record a strong reliance of carbonate deposition on the presence of organic nuclei, supporting carbonate accumulation rates comparable to those in modern reefs. Therefore, the unusual macroscopic morphologies of microbially influenced facies in Neoproterozoic cap carbonates may not reflect oceans that were greatly oversaturated with respect to carbonate minerals.