Abstract Internal loading has long been regarded as an ‘Achilles heel’ in aquatic science and management. Internal loading is of fundamental importance in large and shallow lakes, where even low wind velocities can cause a considerable resuspension of matter deposited on the lake bed. The resuspended matter, and the chemical substances bound to the resuspended matter, will influence almost all processes in the aquatic ecosystem, such as water clarity and depth of the photic zone, and hence, primary and secondary production. If the sediments are contaminated, it will increase the concentrations of harmful substances in water and sediments and the potential ecosystem effects related to such concentrations. This paper presents an overview of the processes regulating bottom dynamic conditions in lakes (erosion, transport, accumulation), provides examples on the role of internal loading within the context of limnology and water management, and presents a new, general approach to quantify internal loading from sediments in lakes. The new approach has been critically tested, being a key factor behind the increase in predictive power of a new generation of lake models meant to be used for practical water management. Internal loading of any water pollutant depends on sedimentation. Sedimentation in this approach is presented as a function of two substance-specific variables, including the fall velocity of the carrier-particles and the particulate fraction (which, by definition, is the only fraction of a water pollutant that can settle out on the lake bed), and three generic variables, including mean depth, suspended particulate matter and ET-areas (areas of erosion and transport). On ET-areas there is, by definition, a discontinuous sedimentation of materials that settles according to Stokes' law. Basically, internal loading is the sum of advective (resuspension) and diffusive transport from the sediments. Resuspension from ET-areas is given as a function of the lake form (a new algorithm based on the volume development) and the age of ET-sediments.