Water clarity is an important attribute of lakes, but climatic effects on clarity remain obscure, because lake physical and chemical conditions generate complex responses. Here, we examine how hydrologic variation influences water clarity (Secchi depth) over 30 yr across 24 lakes in northwest Wisconsin (U.S.A.) along a gradient in lake phosphorus (P) concentration and lake attributes (e.g., depth, area, land use, and trophic status). We took a multivariate time‐series approach to explore shared temporal patterns in Secchi depth among lakes and to evaluate the relative strength of hydrological time‐series (lake level, Palmer Drought Severity Index [PDSI], and antecedent precipitation) as a component of water clarity change. Decadal fluctuations in lake level best explain annual shifts in water clarity, but not precipitation or PDSI. The sign and magnitude of the response varies among lakes by trophic status. Oligotrophic lakes become clearer when lake levels decline, and more turbid when lake levels rise, presumably due to increased watershed loading of dissolved organic matter and nutrients. Dilution and stronger stratification during wet years may drive the opposite response observed in eutrophic lakes, which become clearer in wet years and more turbid during drought. Overall, the water clarity response to lake level increased with P concentration and was more positive in shallow polymictic vs. dimictic lakes. Although further study is required, we suggest that trophic status and lake mixis mediate water clarity's response to lake level fluctuations. We propose that eutrophication not only changes mean lake clarity but also the natural relationship of water clarity to hydrology.