Skeleton properties determine coral survival by influencing the range of hydraulic conditions colonies can withstand, selection of suitable habitat, ability to compete for space and light, repair damage and the overall fitness and ecological success of scleractinian corals. Skeletal properties of 16 coral species comprising 3 growth forms collected from Kenyan coral reef lagoons were investigated and found to vary considerably not only between species but between reefs as well, with corals exposed to both sediment and nutrients showing consistent lower skeleton density and strength but high porosity compared to those from sediment-unaffected reefs. Further, high skeletal density and strength but low porosity values were measured in branching relative to other growth forms. The present findings also suggest that the negative effects of nutrients on skeleton properties may be counteracted by high hydrodynamic energy, resulting in stronger skeletons in high hydrodynamic energy-nutrient-polluted reef habitats relative to pristine reefs. These findings have important ecological and management implications with regard to the existence, persistence, productivity and protective value of reefs, damage risks, maintenance and conservation of biological diversity with respect to future global climate change events. Consequently, appropriate watershed, reef and fisheries management options the impacts of local anthropogenic stresses (sediments, nutrients, overexploitation) would be expected to alleviate the effects of these disturbances and have the potential to minimize future large-scale coral reef damage resulting from increased and frequent global climate change events, such as increased ocean acidification (due to elevated atmospheric CO₂) and sea surface temperature.