Successful management of coastal environments requires reliable monitoring methods and indicators. Besides Chlorophyll-a concentration (Chl-a), water transparency measured as Secchi Depth (ZSD) is widely used in Baltic Sea management for water quality assessment as eutrophication indicator. However, in many coastal waters not only phytoplankton but also coloured dissolved organic matter (CDOM) and suspended particulate matter (SPM) influence the under-water light field, and therefore the ZSD. In this study all three main optical variables(CDOM, Chl-a and SPM [organic and inorganic]) as well as ZSD were measured in three Swedish regions: the Bothnian Sea, the Baltic Proper and the Skagerrak in 2010-2014. Regional multiple regressions with Chl-a, CDOM and inorganic SPM as predictors explained the variations in ZSD well (R2adj = 0.53-0.84). Commonality analyses of the regressions indicated considerable differences between regions regarding the contribution of each factor to the variance, R2adj, in ZSD. CDOM explained most of the variance in the Bothnian Sea and the Skagerrak; in general, Chl-a contributed only modestly to the ZSD. In the Baltic Proper the largest contribution was from the interaction of all three variables. As expected, the link between Chl-a and ZSD was much weaker in the Bothnian Sea with high CDOM absorption and SPM concentration. When applying the Swedish EU Water Framework Directive threshold for Good/Moderate Chl-a status in the models it was shown that ZSD is neither a sufficient indicator for eutrophication, nor for changes in Chl-a. Natural coastal gradients in CDOM and SPM influence the reference conditions for ZSD and other eutrophication indicators, such as the depth distribution of macro-algae. Hence, setting targets for these indicators based on reference Chl-a concentrations and simple Chl-a to ZSD relationships might in some cases be inappropriate and misleading due to overestimation of water transparency under natural conditions.