The Late Oxfordian (Bimammatum Zone) deep-shelf deposits of southern Germany are characterised by abundant reefs that laterally pass into marl-limestone alternations. The bioconstructions are made from three main components, sponges, microbialites and allochthonous sediment. A detailed morphological analysis of sponge-microbialite reefs in the Plettenberg section (Swabian Alb, southern Germany) is combined with investigation of calcareous nannofossil assemblages in laterally correspondent marl-limestone alternations in order to trace the evolution of palaeoenvironmental conditions during reef development. Fluctuations of CaCO₃ content in deep-shelf deposits provides evidence of a succession of small-scale lithological units, generally formed by five to six marl-limestone couplets. Within a small-scale lithological unit, a close link is observed between growth patterns of sponge-microbialite reefs and the changes in the nannofossil assemblage composition. Phases of expansion of the build-ups correspond to carbonate deposits, characterised by a relative dominance of large, oligotrophic nannoplankton species (large Watznaueria britannica, Watznaueria manivitiae and Schizosphaerella spp.). Marly intervals reveal a high relative abundance of small-sized taxa (mainly Lotharingius hauffii, small W. britannica and subordinated Biscutum dorsetensis), and bioconstructions show a net reduction in size, or a total demise. This suggests that the same palaeoenvironmental parameters controlled, at the same time, marl versus limestone deposition, reef growth-phases, and calcareous nannofossil assemblage composition. Successive reef growth-phases recognized within a bioherm are correlated to the limestone hemi-couplets. Each reef growth-phase is composed of several stacked elementary sequences, comprising the following succession: (i) sponge, (ii) microbialites and (iii) carbonate mud. In turn, the microbialitic crust is formed of three successive microbial layers: (1) a fine crust of dense to clotted micrite; (2) a centimetre-scale to multicentimetric columnar layer of clotted to peloidal micrite; (3) a centimetre-scale stromatolitic crust. The passage from an initial dense microbial layer, with numerous microencrusters, to a final stromatolitic crust is interpreted as resulting from an increase of the microbial growth-rate, mainly driven by changes in the accumulation rate. Deep-shelf deposits resulted from changes in platform carbonate production and export basinwards controlled both by sea-level and climate changes. Climate controlled the intensity of carbonate production in shallow-platform environments and export towards the deep-shelf, as well as the trophic conditions of the deep-shelf marine-waters. Low trophic conditions favoured platform carbonate production and export basinwards, and a large development of the sponge-microbialite reefs in the deep-shelf. However, a high carbonate accumulation rate in the deep-shelf was also commonly responsible for the demise of sponge-microbialite reefs. During unfavourable and higher trophic conditions (during marl deposition), reduced development and frequent demise of the sponge-microbialite reefs is observed.