The EU Water Framework and Marine Strategy Framework Directives require that macroalgae are used in status assessments of marine areas. Thus, practical macroalgal indicators are needed. We tested the functionality of cumulative algal cover, covers of late-successional and opportunistic algae, and fraction of opportunistic algae as indicators of eutrophication in the brackish northern Baltic Sea. We found a positive response of cumulative algal cover to increasing Secchi depth that accords with results from earlier studies. However, the increase in cumulative cover was mainly due to an increase in the cover of opportunistic algae, usually considered as a sign of proceeding eutrophication. Therefore, the use of increasing cumulative cover of algae as an indicator of a better status of the marine area is not supported. The effects of increasing Secchi depth on late-successional algae showed positive responses to Secchi depth only at deeper strata, suggesting suitability of deeper areas for monitoring, if late-successional algal cover is used as an indicator. Nitrogen concentration had no effects on algal cover, but decreased the fraction of opportunistics. In general, the fraction of opportunistics was high. Also environmental factors not related to eutrophication had strong effects on macroalgal indicators: the algal cover (both late-successionals and opportunistics) decreased clearly with depth, increased with exposure and we also found a latitudinal gradient within our study area, with increasing algal covers towards higher latitudes. More studies on species responses to eutrophication, enabling a more precise division to eutrophication sensitive vs. tolerant species, could improve the indicators tested.