Water level regulation related to hydroelectric power production and flood prevention is an important hydro-morphological pressure on many watercourses around the world. Fouling of fishing nets in autumn during the open water period and in winter under the ice is a common phenomenon in large Finnish lakes where the water level is regulated. This fouling of fishing nets can sometimes be so extensive that fishing has to be stopped. Based on the practical experiences of fishermen, the main cause for the under-ice fouling has been proposed to be the winter draw-down of water causing low water level and stronger currents in lakes, but no conclusive relationship between fouling and water level regulation has yet been demonstrated. Here we show, using long-term winter data from a boreal lake and short-term netting experiments, that fouling of fishing nets results from increased water draw-down during winter (January–March). Our results also show that fouling of fishing nets takes place only if the high water flow rates are accompanied by an intensive lowering of the water level. We also discuss the relevance of our results to other regulated lakes with ice cover.