Water clarity is a key ecological feature of lakes, integrating intrinsic and extrinsic controls. I evaluate patterns of and controls on long-term variability in water clarity in seven northern Wisconsin lakes studied as part of the North Temperate Lakes Long Term Ecological Research Program. I consider factors regulating water clarity at a range of spatial and temporal scales, including a broad comparison of patterns in a range of lake types, and a focused investigation of dynamics in a single lake.

In a comparison of lakes of different trophic status, the more sensitive measure of light transmission and the driving variables controlling inter- and intra-annual dynamics differed in oligotrophic and dystrophic lakes. Variability in light transmission was best characterized by Secchi depth in the clear-water lakes, and attenuation coefficient in the stained lakes. Inter- and intra-annual variability in water clarity was driven by chlorophyll in most lakes, while dissolved organic carbon (DOC) was important in only one lake. These results contribute toward a comprehensive understanding of drivers of long-term variation in water clarity in lakes of contrasting trophic status.

In clear-water Crystal Lake, mean annual Secchi depths ranged from 6m to 11m with years of high water clarity occurring during years with low phytoplankton biomass. External factors (nutrient loading and climate) did not explain these patterns. Rather, long-term dynamics were related to internal trophic processes that linked dynamics in the phytoplankton with those in the fish and zooplankton. The lake's dominant fish species, the yellow perch, cycled between years when young-of-the-year (YOY) perch were present or absent. The interannual fluctuations in Crystal Lake's water clarity were ultimately linked with these 5-year cycles, with higher water clarity observed when YOY were abundant. Conclusions drawn from a statistical dynamic linear model suggest that oscillations in YOY perch abundance were intrinsically driven by the positive effect of adult perch reproduction and the negative effect of juvenile perch via cannibalism and competition.

In summary, long-term dynamics in all but the most stained of these relatively pristine northern Wisconsin lakes are largely a function of inter-annual variability in algal biomass. In the most oligotrophic lake, long-term fluctuations in algal biomass were in turn a function of cyclic dynamics in yellow perch age structure, which controls water clarity through a trophic cascade. These results link an intrinsically generated population cycle to long-term fluctuations in water clarity.