Due to discharge from acid sulfate (a.s.) soils, watercourses and coastal areas in the Gulf of Bothnia are periodically heavily acidified with high concentrations of potentially toxic metals. Data on water quality from 2005 to 2014 in an embanked lake, an estuary of four rivers in western Finland, showed repeated events with acidic water (pH < 5.5) with high concentrations of Al. Size fractionation and species modeling of Al showed that a significant part of the Al occurred as highly toxic small-size fractions (dissolved < 1 kDa and colloidal 1 kDa—0.45 µm) as free ions and complexed to sulfate. The larval abundance of the burbot (Lota lota L.) was shown to be sensitive to acidity during the wintertime spawning migration and spawning. Bearing in mind the importance of estuaries of the northern Baltic Sea as spawning and nursery areas of fish, the reoccurring failure in the reproduction of fish may cause a more serious threat for the lake and adjacent coastal fish stocks than the spectacular, but less frequent, mass kills of adult fish. This demonstrates the close relationship between climate, hydrology, water geochemistry and the aquatic coastal ecosystem in areas affected by a.s. soils. As the current forecast of climate chance indicates warmer winters with more continuous runoff, the effects can become even more prominent. This study also shows that the annual larvae abundance of burbot may be used as a bioindicator and an instrument for the fisheries for obtaining more comprehensive knowledge of the ecological effects of acidic metal discharge from a.s. soils.