Submerged macrophytes are of key importance for aquatic carbon and nutrient cycling, the provision of food and habitat for diverse aquatic communities and numerous other ecosystem services with links to the majority of Sustainable Development Goals. In shallow lakes and also in lowland rivers, they can stabilize clearwater conditions and prevent phytoplankton blooms. Eutrophication leads to their decline, and a complete loss of macrophytes often occurs above critical thresholds in nutrient loading. This can be accompanied by a shift from clear to turbid, phytoplankton-dominated conditions, in particular in shallow lakes. Shading by periphyton is generally known to play an important role in macrophyte decline during lake eutrophication. However, its role is insufficiently considered during the process of macrophyte recovery after nutrient load reduction. Periphyton shading has also hardly been discussed in studies on charophyte decline in oligo-mesotrophic lakes. This is surprising given the fact that charophytes can be key ecosystem components in these lakes and continue declining despite general efforts to reduce nutrient loading. Our combination of field, experimental and modelling studies clearly revealed that shading by periphyton is important 1) during the re-colonization of eutrophic lakes with submerged macrophytes after nutrient load reduction and 2) for the loss of charophytes from oligomesotrophic temperate hardwater lakes. It can also in part explain the re-colonization pattern newly described for temperate shallow lakes that went through an intermediate phase with clear spring and turbid summer conditions during nutrient load reduction. In addition, we found that zooplankton can significantly reduce periphyton biomass at low phytoplankton availability and that differences in periphyton shading affects the sensitivity of macrophytes to herbivory. In general, periphyton can be controlled by both, top-down and bottom-up mechanisms, but grazer effects were found to be greater than nutrient effects. Our long-term measurements of periphyton biomass in eutrophic Lake Müggelsee (7 seasons in a 20 year period) with high temporal resolution (biweekly) showed that periphyton biomass can be highly dynamic during the period relevant for macrophyte growth in temperate lakes. Recurrent patterns, but with strong interannual changes in the timing of peaks and depressions in periphyton total biomass were found. Net losses of periphyton biomass by grazing in late spring/early summer seemed to open a window of opportunity with increased light availability for macrophyte growth. The start of this “windows”, however, advanced in time during the investigated period (2000-18), potentially due to a warming trend affecting start and intensity of periphyton grazing by chironomid larvae. However, decreased nutrient loading probably contributed to the overall decline in periphyton biomass during the investigated period. In the oligo-mesotrophic lakes, bottom-up control of periphyton by nutrients prevailed and points to a hidden eutrophication of their benthic zones. Overall, our findings 1) advance our mechanistic understanding of factors leading to regime shifts in shallow lakes, 2) challenge the current alternative stable states concept and 3) contribute to an improvement of submerged macrophyte restoration measures applied in both, eutrophic as well as oligo-mesotrophic lakes.