Abstract Breeding waterbird communities have suffered globally from the effects of anthropogenic changes in water quality (especially nutrient enrichment) in recent decades, but few studies have demonstrated the positive effects of restorative actions. Annual breeding waterbird surveys in the period 1977–2005 at two restored southern Danish lake basins (combining nutrient load reduction and biomanipulation) showed an up to five‐fold increase in abundance, and considerable changes in species richness and diversity, following restoration to clear water status in both lakes. Parallel surveys at a third lake, which retained clear water quality throughout, offering a form of natural ‘control', showed no such changes over the same time period. Consistent relationships between breeding waterbird abundance, species richness, and diversity with measures of water clarity (Secchi disc depth, chlorophyll a, and suspended matter) suggest that water clarity mainly drives the relationship; inverse relationships between these measures and total nitrogen and phosphorus were less consistent than for water clarity. The results suggest that an improvement in water clarity plays a key role in restoring breeding waterbird communities and suggest that breeding waterbirds can be indicators of the success of lake restoration projects, but more studies are needed to confirm their wider utility under a variety of conditions.