Eutrophication is a strong driver that modifies coastal areas globally and measures to reduce nutrient input are implemented in many areas. As nutrient concentrations in coastal waters can vary drastically with time and space, quantifying the impacts of the actions taken to reduce eutrophication can be logistically challenging. In this study, we assessed the variation in nutrient concentrations along a coastal eutrophication gradient in the Northern Baltic Sea and estimated whether ephemeral macroalgae can function as bioindicators to reflect long-term water nutrient concentrations. We studied spatial variation in total phosphorus (P) and nitrogen (N) concentrations in two green algal species, Cladophora glomerata and Ulva intestinalis, and temporal variation in nutrient concentrations in C. glomerata. Nutrient concentrations in water and algae showed seasonal and between-year variation along the gradient. Phosphorus and nitrogen concentrations in C. glomerata reflected the preceding (0–4 months) nutrient concentrations in water, while nutrient concentrations in U. intestinalis were less reliable indicators of the current and preceding water nutrient concentrations. While more data is needed to evaluate between-year variation, the results indicate that C. glomerata is a useful tool to assess both the spatial and temporal variation in nutrient run-off from land, especially to complement sparse water nutrient analyses.