SUMMARY 1. The strong stabilising effect of increased submerged macrophytes (charophytes) and benthivorous fish reduction on the clear water state was shown for shallow Lake Veluwe and Lake Wolderwijd.2. The first two links in the chain of relationships from external phosphorus (P) loading to in‐lake total‐P concentrations to chlorophyll a concentrations to water transparency, showed a significant correlation with the areal fraction of coverage with charophytes. Higher coverages lead to (i) lower ratios of the in‐lake total‐P concentration compared with the volume weighted average concentration in the inlet water, indicating a higher retention of P in the presence of charophytes (ii) lower chlorophyll a to total‐P ratios, indicating a positive effect of charophytes on top‐down control of algae, and (iii) higher water transparency because of lower algal turbidity. Transparency further improved as a result of benthivorous fish reduction and a significant positive correlation between non‐algal turbidity and benthivorous fish biomass.3. A model was developed taking into account the inherent variability in precipitation and uncertainties in the empirical relationships determining phosphorus export from stream catchments and other sources and eutrophication variables in the receiving lakes. The model was used to compute (i) probability distributions for in‐lake total‐P, chlorophyll a and Secchi Disc transparency in relation to the coverage with charophytes and benthivorous fish biomass, and (ii) exceedence probabilities with respect to critical values for in‐lake total‐P and water transparency for several management scenarios.4. The effects of an expected rise in external nutrient loading on the in‐lake total‐P and chlorophyll a concentrations and on water transparency can be compensated for by two proposed control measures: (i) extended treatment at a waste water treatment plant directly discharging into Lake Veluwe, and (ii) diverting the outlet of a stream draining a catchment with high fertilisation. The minimal internal charophyte coverage needed to sufficiently stabilise the clear water state and to meet with the objective of a summer mean water transparency of at least 1 m was estimated at well over 30% of the lake area, while the benthivorous fish stock should be maintained at the present level of c. 20 kg ha−1.